9 Cell Fate and Dynamic Processes
This mainline shifts the analysis story from static identity to directional biology. Once cells have been placed in a baseline manifold, the next question is often whether they lie along a continuum, where terminal states sit, and which transitions are supported by the data.
sclet gathers diffusion-based embeddings, lineage inference, velocity, and fate-oriented methods under the same workflow umbrella. The point is not just to expose more algorithms, but to make the dynamics route readable and reusable as one coherent chapter of analysis.
In practice this chapter answers three questions, in the order you are most likely to hit them:
- “I have spliced/unspliced assays — how do I get all the way to fate probabilities?” Start with the trajectory mainline workflow, pass through RNA velocity, then let CellRank convert direction into terminal states and fate probabilities. The
RunTrajectoryWorkflow()section shows the whole chain as one call. - “I already have RegVelo results on a GPU server — how do they connect to CellRank?” Jump to wiring RegVelo into CellRank.
- “How do I tell whether the result is real or a smoke screen?” Read diagnosing the velocity-fate chain. This section makes the diagnostic helpers (
CellRankSummary(),VelocityFateCorrelation(), and their plots) part of the main narrative instead of an afterthought.
All runs along the way write into the same state layer described in state-aware analysis, so every intermediate result can be inspected by id and replayed without recomputation.
9.1 Trajectory mainline workflow
If you do not want to stitch together RunDiffusionMap(), RunSlingshot(), RunVelocity(), and RunCellFate() by hand every time, sclet now provides RunTrajectoryWorkflow() as the semantic entry point for this entire analysis mainline.
The point of this wrapper is not to hide the underlying methods. The point is to make the recommended analysis path easier to follow, easier to document, and easier to rerun later.
panc_main <- readRDS("data/pancreas_sub_sce.rds")
panc_main <- RunTrajectoryWorkflow(
panc_main,
group = "SubCellType",
reduction = "UMAP",
run_diffusion_map = TRUE,
run_slingshot = TRUE,
run_velocity = "never",
run_fate = "never",
name = "pancreas_main"
)## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## 'as(<dsCMatrix>, "dgTMatrix")' is deprecated.
## Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead.
## See help("Deprecated") and help("Matrix-deprecated").## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'
panc <- readRDS("data/pancreas_sub_sce.rds")
panc <- RunSlingshot(sce = panc, group = "SubCellType", reduction = "UMAP")## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'RunSlingshot() writes its result back into the unified state layer, so downstream helpers such as plot_lineage() and plot_pseudotime() can consume the recorded trajectory object directly. If needed, you can also check has_trajectory(panc) or inspect get_trajectory(panc).
If you keep multiple trajectory runs in the same object, give them different name values and inspect them explicitly with get_trajectory(panc, id = "your_id").
9.1.1 Lineage plot
p1 <- plot_lineage(panc, group = "SubCellType") +
sc_dim_geom_label(
geom = shadowtext::geom_shadowtext,
color='black',
bg.color='white'
)## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## displayed selected lineages
p2 <- plot_lineage(panc, group = "SubCellType", lineages = c("Lineage1", "Lineage2")) +
sc_dim_geom_label(
geom = shadowtext::geom_shadowtext,
color='black',
bg.color='white'
)## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'
9.1.2 Pseudotime plot
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
9.1.3 Expression trends in different cell trajectories
curve_genes <- c("Mrpl15", "Tram1", "Ncoa2")
## 默认选取smooth方法直接拟合得到的基因表达值结果来画图
p_curve <- plot_genecurve(panc, features = curve_genes, method = "smooth")
## 也可以用GAM计算预测的基因表达值来画图
p_curve1 <- plot_genecurve(panc, features = curve_genes, method = "gam")
plot_list(p_curve, p_curve1, ncol=1)## `geom_smooth()` using method = 'loess' and formula = 'y ~
## x'
9.1.4 Heatmap
heatmap_genes <- head(unique(rownames(panc)), 10)
## 默认按照拟时间排序
hmp1 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2")
## 可以手动对基因或细胞设置聚类(cluster = TRUE)，此时会打乱pseudotime的排序
hmp2 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2", cluster_columns = TRUE)
## 对基因聚类
hmp3 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2", cluster_rows = TRUE, sort = FALSE)
## 默认排序
hmp4 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2", cluster_rows = FALSE, sort = TRUE)
## 组合起来看就能看到两个参数的设定对行顺序的影响
plot_list(hmp1, hmp2, hmp3, hmp4, ncol=1)
9.2 Diffusion Map for complex trajectories
For very continuous developmental systems, PCA and UMAP are often convenient but not always topology-faithful. RunDiffusionMap() adds a diffusion-based representation that can be tracked like any other reduction in sclet, which is useful when you want a more trajectory-aware geometry before moving on to downstream lineage tools.
panc_dm <- panc
if (!"logcounts" %in% SummarizedExperiment::assayNames(panc_dm) &&
"counts" %in% SummarizedExperiment::assayNames(panc_dm)) {
panc_dm <- NormalizeData(panc_dm)
}
if (!"PCA" %in% SingleCellExperiment::reducedDimNames(panc_dm)) {
dm_features <- rownames(panc_dm)[seq_len(min(500, nrow(panc_dm)))]
dm_layer <- if ("logcounts" %in% SummarizedExperiment::assayNames(panc_dm)) "logcounts" else "counts"
panc_dm <- RunPCA(panc_dm, subset_row = dm_features, layer = dm_layer)
}## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## DC_1 DC_2 DC_3
## CAGCCGAAGCGATATA -0.04762849 -0.02534582 0.0127494749
## AGTGTCATCGCCGTGA 0.01191557 0.05261432 0.0003914782
## GATGAAAAGTTGTAGA -0.04810711 -0.02576844 0.0139306400
## CACAGTACATCCGTGG 0.02733252 -0.01166796 0.0152364853
## CGGAGCTCATTGGGCC -0.04534807 -0.01974909 0.0065963459
## AGAGCTTGTGTGACCC -0.03782034 -0.01332305 0.0002428841## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'
The velocity and CellRank examples in this section use cached objects generated by the update-data-velocity-fate GitHub Actions workflow. This keeps the book render lightweight: Python-backed basilisk, velociraptor, and CellRank work is done in the data-update workflow, while the book only reads the resulting RDS files.
RNA metabolic process:
- RNA is synthesized at a rate of alpha
- RNA is spliced to remove introns and form mature mRNA at rate of beta
- Mature mRNA is degraded after functioning at rate of gamma
The disruption of the equilibrium between unspliced and spliced RNA indicates whether a gene is in an induced or repressed state.
With RNA-seq, especially the Poly-A enrichment method, the propotion of unspliced RNA obtained is relatively small. Currently, there are also some techinques capable of enriching nascent RNA in single cells, such as scSLAM-seq and scNT-seq.
Although some researchers are skeptical about RNA velocity, it has received significant attention because it can automatically detect the direction of trajectories.
scVelo supports a full dynamical model and various of utility functions (Bergen et al. 2020). It only supports Python and can be run in R using velociraptor.
9.2.1 Example data
This example is adopted from https://www.bioconductor.org/packages/devel/bioc/vignettes/velociraptor/inst/doc/velociraptor.html.
## class: SingleCellExperiment
## dim: 2000 300
## metadata(2): sclet sclet_bookdown_cache
## assays(3): spliced unspliced logcounts
## rownames(2000): ENSMUSG00000117819.1
## ENSMUSG00000081984.3 ... ENSMUSG00000087185.1
## ENSMUSG00000086732.1
## rowData names(0):
## colnames(300): CCCATACTCCGAAGAG AATCCAGTCATCTGCC ...
## GCGCGATAGGCTCATT CTAAGACTCACTATTC
## colData names(11): celltype sizeFactor ...
## cellrank_fate_X0 cellrank_fate_X1## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## reducedDimNames(3): PCA .dimred UMAP
## mainExpName: NULL## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## altExpNames(0):## [1] "ENSMUSG00000117819.1" "ENSMUSG00000081984.3"
## [3] "ENSMUSG00000047995.7" "ENSMUSG00000060860.8"
## [5] "ENSMUSG00000100153.2" "ENSMUSG00000090137.8"9.2.2 Run velocity analysis
sclet wraps the RNA velocity inference via RunVelocity(). Under the hood, it delegates the heavy lifting to scVelo (managed safely via the basilisk/velociraptor Python sandbox) and smoothly registers the outputs to the velocity analysis state.
## $id
## [1] "velocity"
##
## $type
## [1] "velocity"
##
## $status
## [1] "completed"
##
## $method
## [1] "velociraptor::scvelo"
##
## $inputs
## $inputs$assays
## [1] "spliced" "unspliced"
##
## $inputs$reduction
## [1] "PCA"
##
##
## $artifacts
## $artifacts$analysis_key
## [1] "velocity"
##
## $artifacts$colData
## [1] "velocity_pseudotime" "velocity_confidence"
## [3] "root_cells" "end_points"
##
## $artifacts$reductions
## character(0)
##
##
## $params
## $params$mode
## [1] "deterministic"
##
## $params$subset.row
## [1] "ENSMUSG00000117819.1" "ENSMUSG00000081984.3"
## [3] "ENSMUSG00000047995.7" "ENSMUSG00000060860.8"
## [5] "ENSMUSG00000100153.2" "ENSMUSG00000090137.8"
## [7] "ENSMUSG00000064220.6" "ENSMUSG00000064351.1"
## [9] "ENSMUSG00000063954.7" "ENSMUSG00000027505.2"
## [11] "ENSMUSG00000059695.4" "ENSMUSG00000038994.6"
## [13] "ENSMUSG00000027431.5" "ENSMUSG00000018543.8"
## [15] "ENSMUSG00000105734.1" "ENSMUSG00000042800.5"
## [17] "ENSMUSG00000022832.11" "ENSMUSG00000048686.4"
## [19] "ENSMUSG00000100937.1" "ENSMUSG00000028259.13"
## [21] "ENSMUSG00000030976.3" "ENSMUSG00000079710.10"
## [23] "ENSMUSG00000020483.14" "ENSMUSG00000094624.1"
## [25] "ENSMUSG00000031512.15" "ENSMUSG00000078577.3"
## [27] "ENSMUSG00000078554.2" "ENSMUSG00000048077.6"
## [29] "ENSMUSG00000008482.9" "ENSMUSG00000079666.8"
## [31] "ENSMUSG00000041399.3" "ENSMUSG00000029867.5"
## [33] "ENSMUSG00000027564.4" "ENSMUSG00000070708.5"
## [35] "ENSMUSG00000050621.7" "ENSMUSG00000031991.10"
## [37] "ENSMUSG00000009093.7" "ENSMUSG00000047129.11"
## [39] "ENSMUSG00000085861.1" "ENSMUSG00000025482.11"
## [41] "ENSMUSG00000020286.12" "ENSMUSG00000062154.14"
## [43] "ENSMUSG00000050058.6" "ENSMUSG00000095384.1"
## [45] "ENSMUSG00000051276.4" "ENSMUSG00000045521.7"
## [47] "ENSMUSG00000028264.16" "ENSMUSG00000029723.16"
## [49] "ENSMUSG00000053184.15" "ENSMUSG00000118396.2"
## [51] "ENSMUSG00000021838.17" "ENSMUSG00000029433.16"
## [53] "ENSMUSG00000047841.8" "ENSMUSG00000057072.11"
## [55] "ENSMUSG00000066383.7" "ENSMUSG00000062028.8"
## [57] "ENSMUSG00000044444.6" "ENSMUSG00000047843.16"
## [59] "ENSMUSG00000079346.4" "ENSMUSG00000027938.11"
## [61] "ENSMUSG00000063971.7" "ENSMUSG00000041673.12"
## [63] "ENSMUSG00000045709.11" "ENSMUSG00000028938.9"
## [65] "ENSMUSG00000101959.1" "ENSMUSG00000099863.1"
## [67] "ENSMUSG00000032900.15" "ENSMUSG00000027442.10"
## [69] "ENSMUSG00000038691.5" "ENSMUSG00000064357.1"
## [71] "ENSMUSG00000046755.5" "ENSMUSG00000024233.10"
## [73] "ENSMUSG00000008393.9" "ENSMUSG00000020617.13"
## [75] "ENSMUSG00000044526.3" "ENSMUSG00000020945.13"
## [77] "ENSMUSG00000043629.12" "ENSMUSG00000074748.3"
## [79] "ENSMUSG00000066500.5" "ENSMUSG00000049916.12"
## [81] "ENSMUSG00000032803.15" "ENSMUSG00000068240.5"
## [83] "ENSMUSG00000055826.5" "ENSMUSG00000038523.10"
## [85] "ENSMUSG00000059455.3" "ENSMUSG00000048731.15"
## [87] "ENSMUSG00000044056.3" "ENSMUSG00000024430.14"
## [89] "ENSMUSG00000051113.9" "ENSMUSG00000095040.2"
## [91] "ENSMUSG00000030714.14" "ENSMUSG00000070489.5"
## [93] "ENSMUSG00000030859.8" "ENSMUSG00000022148.16"
## [95] "ENSMUSG00000053375.8" "ENSMUSG00000041566.3"
## [97] "ENSMUSG00000064358.1" "ENSMUSG00000061477.4"
## [99] "ENSMUSG00000100282.1" "ENSMUSG00000036438.14"
## [101] "ENSMUSG00000067909.4" "ENSMUSG00000021545.5"
## [103] "ENSMUSG00000054523.13" "ENSMUSG00000031682.5"
## [105] "ENSMUSG00000045942.13" "ENSMUSG00000090117.7"
## [107] "ENSMUSG00000037307.11" "ENSMUSG00000050685.5"
## [109] "ENSMUSG00000038709.14" "ENSMUSG00000014301.13"
## [111] "ENSMUSG00000024501.20" "ENSMUSG00000037708.16"
## [113] "ENSMUSG00000059288.14" "ENSMUSG00000064341.1"
## [115] "ENSMUSG00000100862.1" "ENSMUSG00000027674.16"
## [117] "ENSMUSG00000027355.15" "ENSMUSG00000074344.7"
## [119] "ENSMUSG00000073758.10" "ENSMUSG00000027886.7"
## [121] "ENSMUSG00000070563.6" "ENSMUSG00000055553.16"
## [123] "ENSMUSG00000026963.4" "ENSMUSG00000021768.15"
## [125] "ENSMUSG00000101111.1" "ENSMUSG00000041540.16"
## [127] "ENSMUSG00000030858.10" "ENSMUSG00000005803.14"
## [129] "ENSMUSG00000109864.1" "ENSMUSG00000056509.10"
## [131] "ENSMUSG00000091396.2" "ENSMUSG00000047150.8"
## [133] "ENSMUSG00000074435.10" "ENSMUSG00000069971.5"
## [135] "ENSMUSG00000089989.10" "ENSMUSG00000010435.7"
## [137] "ENSMUSG00000037689.6" "ENSMUSG00000027606.12"
## [139] "ENSMUSG00000029477.14" "ENSMUSG00000026592.13"
## [141] "ENSMUSG00000058935.14" "ENSMUSG00000035085.5"
## [143] "ENSMUSG00000060491.14" "ENSMUSG00000095159.2"
## [145] "ENSMUSG00000026809.15" "ENSMUSG00000095869.1"
## [147] "ENSMUSG00000049154.12" "ENSMUSG00000048655.17"
## [149] "ENSMUSG00000046173.3" "ENSMUSG00000021961.6"
## [151] "ENSMUSG00000026864.13" "ENSMUSG00000095789.6"
## [153] "ENSMUSG00000045336.5" "ENSMUSG00000020234.10"
## [155] "ENSMUSG00000001558.5" "ENSMUSG00000031452.15"
## [157] "ENSMUSG00000055692.21" "ENSMUSG00000023467.18"
## [159] "ENSMUSG00000026827.12" "ENSMUSG00000050141.13"
## [161] "ENSMUSG00000043050.8" "ENSMUSG00000021415.13"
## [163] "ENSMUSG00000019876.15" "ENSMUSG00000063480.8"
## [165] "ENSMUSG00000036924.3" "ENSMUSG00000052920.16"
## [167] "ENSMUSG00000013091.5" "ENSMUSG00000086361.1"
## [169] "ENSMUSG00000073380.2" "ENSMUSG00000049761.6"
## [171] "ENSMUSG00000033949.12" "ENSMUSG00000116210.1"
## [173] "ENSMUSG00000073731.12" "ENSMUSG00000047025.5"
## [175] "ENSMUSG00000030161.8" "ENSMUSG00000040883.18"
## [177] "ENSMUSG00000006941.5" "ENSMUSG00000072772.3"
## [179] "ENSMUSG00000041791.6" "ENSMUSG00000100684.1"
## [181] "ENSMUSG00000043633.6" "ENSMUSG00000027496.15"
## [183] "ENSMUSG00000047518.3" "ENSMUSG00000048573.9"
## [185] "ENSMUSG00000023257.3" "ENSMUSG00000064354.1"
## [187] "ENSMUSG00000078127.3" "ENSMUSG00000090840.2"
## [189] "ENSMUSG00000022249.14" "ENSMUSG00000020460.15"
## [191] "ENSMUSG00000095867.2" "ENSMUSG00000043859.5"
## [193] "ENSMUSG00000028141.11" "ENSMUSG00000110464.1"
## [195] "ENSMUSG00000059430.14" "ENSMUSG00000047108.4"
## [197] "ENSMUSG00000021585.10" "ENSMUSG00000020270.9"
## [199] "ENSMUSG00000101796.1" "ENSMUSG00000049694.13"
## [201] "ENSMUSG00000026969.3" "ENSMUSG00000024397.14"
## [203] "ENSMUSG00000026182.6" "ENSMUSG00000034913.10"
## [205] "ENSMUSG00000061474.11" "ENSMUSG00000044122.15"
## [207] "ENSMUSG00000028575.11" "ENSMUSG00000021534.8"
## [209] "ENSMUSG00000117852.1" "ENSMUSG00000030421.9"
## [211] "ENSMUSG00000036167.16" "ENSMUSG00000039555.14"
## [213] "ENSMUSG00000017767.3" "ENSMUSG00000009115.5"
## [215] "ENSMUSG00000036244.5" "ENSMUSG00000035522.3"
## [217] "ENSMUSG00000008307.11" "ENSMUSG00000026226.16"
## [219] "ENSMUSG00000050641.7" "ENSMUSG00000102070.1"
## [221] "ENSMUSG00000028427.13" "ENSMUSG00000032530.14"
## [223] "ENSMUSG00000048206.6" "ENSMUSG00000061633.3"
## [225] "ENSMUSG00000007907.4" "ENSMUSG00000004633.17"
## [227] "ENSMUSG00000046957.5" "ENSMUSG00000022501.6"
## [229] "ENSMUSG00000027480.12" "ENSMUSG00000030629.15"
## [231] "ENSMUSG00000020622.17" "ENSMUSG00000089781.2"
## [233] "ENSMUSG00000040541.8" "ENSMUSG00000026940.3"
## [235] "ENSMUSG00000099353.7" "ENSMUSG00000046750.17"
## [237] "ENSMUSG00000021203.15" "ENSMUSG00000070999.2"
## [239] "ENSMUSG00000062651.4" "ENSMUSG00000033213.16"
## [241] "ENSMUSG00000101894.1" "ENSMUSG00000045378.5"
## [243] "ENSMUSG00000020940.13" "ENSMUSG00000090202.1"
## [245] "ENSMUSG00000002240.12" "ENSMUSG00000031509.10"
## [247] "ENSMUSG00000019945.10" "ENSMUSG00000030344.11"
## [249] "ENSMUSG00000038015.6" "ENSMUSG00000038180.11"
## [251] "ENSMUSG00000070332.4" "ENSMUSG00000067367.9"
## [253] "ENSMUSG00000017720.2" "ENSMUSG00000097522.1"
## [255] "ENSMUSG00000012405.16" "ENSMUSG00000085940.1"
## [257] "ENSMUSG00000032110.4" "ENSMUSG00000090273.3"
## [259] "ENSMUSG00000078161.8" "ENSMUSG00000001175.15"
## [261] "ENSMUSG00000048994.2" "ENSMUSG00000058173.12"
## [263] "ENSMUSG00000007591.15" "ENSMUSG00000024059.10"
## [265] "ENSMUSG00000055891.7" "ENSMUSG00000004455.16"
## [267] "ENSMUSG00000050089.13" "ENSMUSG00000066878.5"
## [269] "ENSMUSG00000041068.6" "ENSMUSG00000038997.4"
## [271] "ENSMUSG00000030206.13" "ENSMUSG00000070392.5"
## [273] "ENSMUSG00000028332.13" "ENSMUSG00000062867.13"
## [275] "ENSMUSG00000043036.13" "ENSMUSG00000116615.1"
## [277] "ENSMUSG00000029678.8" "ENSMUSG00000002308.16"
## [279] "ENSMUSG00000003518.13" "ENSMUSG00000062825.15"
## [281] "ENSMUSG00000020096.20" "ENSMUSG00000089743.7"
## [283] "ENSMUSG00000028484.16" "ENSMUSG00000030385.4"
## [285] "ENSMUSG00000029909.6" "ENSMUSG00000026931.10"
## [287] "ENSMUSG00000030077.11" "ENSMUSG00000021499.12"
## [289] "ENSMUSG00000058690.14" "ENSMUSG00000090206.8"
## [291] "ENSMUSG00000045004.3" "ENSMUSG00000022982.10"
## [293] "ENSMUSG00000070979.5" "ENSMUSG00000040681.16"
## [295] "ENSMUSG00000094975.1" "ENSMUSG00000014529.9"
## [297] "ENSMUSG00000062075.13" "ENSMUSG00000021590.7"
## [299] "ENSMUSG00000040456.2" "ENSMUSG00000029682.5"
## [301] "ENSMUSG00000022674.15" "ENSMUSG00000022993.7"
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## [889] "ENSMUSG00000052525.14" "ENSMUSG00000096573.2"
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## [893] "ENSMUSG00000038244.14" "ENSMUSG00000106445.1"
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## [897] "ENSMUSG00000048400.13" "ENSMUSG00000050592.8"
## [899] "ENSMUSG00000067101.5" "ENSMUSG00000004897.16"
## [901] "ENSMUSG00000094592.1" "ENSMUSG00000005148.8"
## [903] "ENSMUSG00000042607.15" "ENSMUSG00000033053.4"
## [905] "ENSMUSG00000022657.9" "ENSMUSG00000033502.15"
## [907] "ENSMUSG00000068506.3" "ENSMUSG00000021114.9"
## [909] "ENSMUSG00000022400.9" "ENSMUSG00000112913.1"
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## [913] "ENSMUSG00000084901.6" "ENSMUSG00000087611.1"
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## [917] "ENSMUSG00000091311.3" "ENSMUSG00000074224.3"
## [919] "ENSMUSG00000030403.9" "ENSMUSG00000043319.5"
## [921] "ENSMUSG00000048416.15" "ENSMUSG00000025231.17"
## [923] "ENSMUSG00000085961.1" "ENSMUSG00000089730.2"
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## [927] "ENSMUSG00000043945.4" "ENSMUSG00000074139.8"
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## [933] "ENSMUSG00000048445.6" "ENSMUSG00000029766.7"
## [935] "ENSMUSG00000085037.1" "ENSMUSG00000028845.15"
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## [941] "ENSMUSG00000091147.1" "ENSMUSG00000044502.16"
## [943] "ENSMUSG00000107988.1" "ENSMUSG00000027562.12"
## [945] "ENSMUSG00000089984.7" "ENSMUSG00000073141.8"
## [947] "ENSMUSG00000024712.9" "ENSMUSG00000106086.1"
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## [951] "ENSMUSG00000025794.9" "ENSMUSG00000025245.14"
## [953] "ENSMUSG00000038503.15" "ENSMUSG00000022800.14"
## [955] "ENSMUSG00000094052.2" "ENSMUSG00000107141.1"
## [957] "ENSMUSG00000045193.13" "ENSMUSG00000030189.15"
## [959] "ENSMUSG00000099923.2" "ENSMUSG00000093993.7"
## [961] "ENSMUSG00000024193.8" "ENSMUSG00000020462.14"
## [963] "ENSMUSG00000094802.7" "ENSMUSG00000022744.12"
## [965] "ENSMUSG00000096468.7" "ENSMUSG00000024853.10"
## [967] "ENSMUSG00000040888.10" "ENSMUSG00000110665.1"
## [969] "ENSMUSG00000074677.11" "ENSMUSG00000025156.17"
## [971] "ENSMUSG00000020415.16" "ENSMUSG00000106741.3"
## [973] "ENSMUSG00000028441.12" "ENSMUSG00000013593.12"
## [975] "ENSMUSG00000096867.1" "ENSMUSG00000048039.8"
## [977] "ENSMUSG00000038570.15" "ENSMUSG00000029229.8"
## [979] "ENSMUSG00000020180.10" "ENSMUSG00000031085.16"
## [981] "ENSMUSG00000092074.2" "ENSMUSG00000024217.10"
## [983] "ENSMUSG00000029620.4" "ENSMUSG00000055943.5"
## [985] "ENSMUSG00000056912.12" "ENSMUSG00000029155.16"
## [987] "ENSMUSG00000004667.18" "ENSMUSG00000055882.8"
## [989] "ENSMUSG00000087250.2" "ENSMUSG00000043421.8"
## [991] "ENSMUSG00000100708.1" "ENSMUSG00000035133.9"
## [993] "ENSMUSG00000052099.14" "ENSMUSG00000024663.20"
## [995] "ENSMUSG00000024905.15" "ENSMUSG00000000171.5"
## [997] "ENSMUSG00000115761.1" "ENSMUSG00000024758.15"
## [999] "ENSMUSG00000000579.14" "ENSMUSG00000044957.3"
## [1001] "ENSMUSG00000026585.13" "ENSMUSG00000028572.13"
## [1003] "ENSMUSG00000104960.1" "ENSMUSG00000107073.1"
## [1005] "ENSMUSG00000001687.15" "ENSMUSG00000059447.13"
## [1007] "ENSMUSG00000037072.15" "ENSMUSG00000023873.13"
## [1009] "ENSMUSG00000100837.7" "ENSMUSG00000079652.8"
## [1011] "ENSMUSG00000026989.5" "ENSMUSG00000063089.4"
## [1013] "ENSMUSG00000031181.2" "ENSMUSG00000042396.10"
## [1015] "ENSMUSG00000020844.6" "ENSMUSG00000040990.17"
## [1017] "ENSMUSG00000051185.9" "ENSMUSG00000034813.18"
## [1019] "ENSMUSG00000051732.2" "ENSMUSG00000090457.3"
## [1021] "ENSMUSG00000087524.1" "ENSMUSG00000042564.13"
## [1023] "ENSMUSG00000028132.15" "ENSMUSG00000030069.15"
## [1025] "ENSMUSG00000099531.1" "ENSMUSG00000029602.11"
## [1027] "ENSMUSG00000059690.1" "ENSMUSG00000027409.5"
## [1029] "ENSMUSG00000006715.11" "ENSMUSG00000022769.9"
## [1031] "ENSMUSG00000103840.1" "ENSMUSG00000006143.12"
## [1033] "ENSMUSG00000079334.8" "ENSMUSG00000068686.12"
## [1035] "ENSMUSG00000025724.12" "ENSMUSG00000083896.8"
## [1037] "ENSMUSG00000038696.14" "ENSMUSG00000043153.6"
## [1039] "ENSMUSG00000020420.8" "ENSMUSG00000017802.14"
## [1041] "ENSMUSG00000070883.3" "ENSMUSG00000030647.8"
## [1043] "ENSMUSG00000027985.14" "ENSMUSG00000100557.1"
## [1045] "ENSMUSG00000022141.7" "ENSMUSG00000100372.1"
## [1047] "ENSMUSG00000060794.8" "ENSMUSG00000029191.16"
## [1049] "ENSMUSG00000042726.14" "ENSMUSG00000058603.10"
## [1051] "ENSMUSG00000038347.15" "ENSMUSG00000091255.1"
## [1053] "ENSMUSG00000019996.17" "ENSMUSG00000099740.1"
## [1055] "ENSMUSG00000032171.7" "ENSMUSG00000080725.9"
## [1057] "ENSMUSG00000061689.15" "ENSMUSG00000024145.6"
## [1059] "ENSMUSG00000034165.16" "ENSMUSG00000096001.2"
## [1061] "ENSMUSG00000025486.17" "ENSMUSG00000060073.9"
## [1063] "ENSMUSG00000096769.7" "ENSMUSG00000059972.7"
## [1065] "ENSMUSG00000095413.1" "ENSMUSG00000029685.15"
## [1067] "ENSMUSG00000051437.4" "ENSMUSG00000034706.16"
## [1069] "ENSMUSG00000058183.14" "ENSMUSG00000020624.3"
## [1071] "ENSMUSG00000094811.7" "ENSMUSG00000101683.6"
## [1073] "ENSMUSG00000027459.16" "ENSMUSG00000034192.5"
## [1075] "ENSMUSG00000054405.14" "ENSMUSG00000071041.4"
## [1077] "ENSMUSG00000026966.6" "ENSMUSG00000096650.7"
## [1079] "ENSMUSG00000052748.14" "ENSMUSG00000073795.11"
## [1081] "ENSMUSG00000087260.5" "ENSMUSG00000110332.1"
## [1083] "ENSMUSG00000034473.14" "ENSMUSG00000055302.5"
## [1085] "ENSMUSG00000054115.11" "ENSMUSG00000014470.4"
## [1087] "ENSMUSG00000027341.10" "ENSMUSG00000096372.1"
## [1089] "ENSMUSG00000068219.8" "ENSMUSG00000029423.10"
## [1091] "ENSMUSG00000101051.6" "ENSMUSG00000021337.8"
## [1093] "ENSMUSG00000039704.7" "ENSMUSG00000047441.4"
## [1095] "ENSMUSG00000049339.16" "ENSMUSG00000069041.8"
## [1097] "ENSMUSG00000025613.13" "ENSMUSG00000005233.16"
## [1099] "ENSMUSG00000034031.5" "ENSMUSG00000034401.16"
## [1101] "ENSMUSG00000038095.15" "ENSMUSG00000090935.10"
## [1103] "ENSMUSG00000003166.20" "ENSMUSG00000073001.3"
## [1105] "ENSMUSG00000029564.12" "ENSMUSG00000025043.3"
## [1107] "ENSMUSG00000038594.9" "ENSMUSG00000052906.7"
## [1109] "ENSMUSG00000021572.9" "ENSMUSG00000072692.7"
## [1111] "ENSMUSG00000092519.2" "ENSMUSG00000022174.8"
## [1113] "ENSMUSG00000032294.17" "ENSMUSG00000036480.9"
## [1115] "ENSMUSG00000015222.18" "ENSMUSG00000029701.15"
## [1117] "ENSMUSG00000116554.1" "ENSMUSG00000030465.19"
## [1119] "ENSMUSG00000035578.16" "ENSMUSG00000022021.14"
## [1121] "ENSMUSG00000043060.8" "ENSMUSG00000090685.1"
## [1123] "ENSMUSG00000022892.11" "ENSMUSG00000033307.7"
## [1125] "ENSMUSG00000031919.6" "ENSMUSG00000020018.6"
## [1127] "ENSMUSG00000029550.11" "ENSMUSG00000071788.5"
## [1129] "ENSMUSG00000049881.13" "ENSMUSG00000028868.13"
## [1131] "ENSMUSG00000003200.10" "ENSMUSG00000035232.8"
## [1133] "ENSMUSG00000022972.10" "ENSMUSG00000026339.18"
## [1135] "ENSMUSG00000023051.11" "ENSMUSG00000097424.2"
## [1137] "ENSMUSG00000114412.1" "ENSMUSG00000036921.2"
## [1139] "ENSMUSG00000036463.8" "ENSMUSG00000102416.4"
## [1141] "ENSMUSG00000053914.9" "ENSMUSG00000107214.3"
## [1143] "ENSMUSG00000091906.2" "ENSMUSG00000036574.5"
## [1145] "ENSMUSG00000100963.1" "ENSMUSG00000021483.8"
## [1147] "ENSMUSG00000054717.7" "ENSMUSG00000032671.5"
## [1149] "ENSMUSG00000042672.15" "ENSMUSG00000042320.17"
## [1151] "ENSMUSG00000025287.15" "ENSMUSG00000006412.10"
## [1153] "ENSMUSG00000107478.1" "ENSMUSG00000116976.1"
## [1155] "ENSMUSG00000033102.15" "ENSMUSG00000000247.11"
## [1157] "ENSMUSG00000020904.11" "ENSMUSG00000029003.11"
## [1159] "ENSMUSG00000041923.15" "ENSMUSG00000031782.15"
## [1161] "ENSMUSG00000112654.1" "ENSMUSG00000093950.2"
## [1163] "ENSMUSG00000066979.6" "ENSMUSG00000101801.6"
## [1165] "ENSMUSG00000033963.16" "ENSMUSG00000086898.1"
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## [1169] "ENSMUSG00000002043.17" "ENSMUSG00000059395.4"
## [1171] "ENSMUSG00000037573.5" "ENSMUSG00000103328.1"
## [1173] "ENSMUSG00000020214.10" "ENSMUSG00000070283.4"
## [1175] "ENSMUSG00000101155.6" "ENSMUSG00000100121.1"
## [1177] "ENSMUSG00000106013.4" "ENSMUSG00000049354.8"
## [1179] "ENSMUSG00000022753.15" "ENSMUSG00000079299.3"
## [1181] "ENSMUSG00000037017.15" "ENSMUSG00000094294.2"
## [1183] "ENSMUSG00000032204.13" "ENSMUSG00000100240.1"
## [1185] "ENSMUSG00000100431.2" "ENSMUSG00000049491.15"
## [1187] "ENSMUSG00000094258.7" "ENSMUSG00000020633.14"
## [1189] "ENSMUSG00000031458.8" "ENSMUSG00000089982.7"
## [1191] "ENSMUSG00000035021.13" "ENSMUSG00000030990.18"
## [1193] "ENSMUSG00000028451.12" "ENSMUSG00000085486.2"
## [1195] "ENSMUSG00000026523.14" "ENSMUSG00000004341.8"
## [1197] "ENSMUSG00000002228.7" "ENSMUSG00000031608.13"
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## [1203] "ENSMUSG00000101915.1" "ENSMUSG00000028383.17"
## [1205] "ENSMUSG00000083287.4" "ENSMUSG00000025903.14"
## [1207] "ENSMUSG00000070493.3" "ENSMUSG00000033174.17"
## [1209] "ENSMUSG00000037001.10" "ENSMUSG00000059208.15"
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## [1213] "ENSMUSG00000002957.11" "ENSMUSG00000056815.1"
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## [1229] "ENSMUSG00000050087.3" "ENSMUSG00000093752.1"
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## [1243] "ENSMUSG00000086587.7" "ENSMUSG00000031818.12"
## [1245] "ENSMUSG00000056260.15" "ENSMUSG00000027099.9"
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## [1255] "ENSMUSG00000007739.10" "ENSMUSG00000034248.7"
## [1257] "ENSMUSG00000024959.14" "ENSMUSG00000021986.9"
## [1259] "ENSMUSG00000038515.10" "ENSMUSG00000026778.13"
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## [1273] "ENSMUSG00000030978.10" "ENSMUSG00000018362.14"
## [1275] "ENSMUSG00000008855.17" "ENSMUSG00000026729.9"
## [1277] "ENSMUSG00000028789.16" "ENSMUSG00000096016.7"
## [1279] "ENSMUSG00000117104.1" "ENSMUSG00000109228.2"
## [1281] "ENSMUSG00000069118.3" "ENSMUSG00000037236.16"
## [1283] "ENSMUSG00000090307.7" "ENSMUSG00000085197.7"
## [1285] "ENSMUSG00000032238.17" "ENSMUSG00000051329.13"
## [1287] "ENSMUSG00000032177.17" "ENSMUSG00000028389.12"
## [1289] "ENSMUSG00000044795.12" "ENSMUSG00000024317.15"
## [1291] "ENSMUSG00000002210.11" "ENSMUSG00000029103.16"
## [1293] "ENSMUSG00000115656.1" "ENSMUSG00000032475.15"
## [1295] "ENSMUSG00000035293.13" "ENSMUSG00000100336.1"
## [1297] "ENSMUSG00000036427.5" "ENSMUSG00000092586.8"
## [1299] "ENSMUSG00000026499.5" "ENSMUSG00000022884.15"
## [1301] "ENSMUSG00000091792.1" "ENSMUSG00000100559.1"
## [1303] "ENSMUSG00000057047.5" "ENSMUSG00000021977.11"
## [1305] "ENSMUSG00000094845.2" "ENSMUSG00000039179.13"
## [1307] "ENSMUSG00000085660.1" "ENSMUSG00000068391.8"
## [1309] "ENSMUSG00000095493.2" "ENSMUSG00000027520.15"
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## [1313] "ENSMUSG00000060161.9" "ENSMUSG00000032221.14"
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## [1317] "ENSMUSG00000006310.10" "ENSMUSG00000035142.18"
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## [1323] "ENSMUSG00000093923.7" "ENSMUSG00000080268.4"
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## [1331] "ENSMUSG00000047215.14" "ENSMUSG00000066278.6"
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## [1337] "ENSMUSG00000041355.13" "ENSMUSG00000038150.7"
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## [1341] "ENSMUSG00000099894.1" "ENSMUSG00000058022.14"
## [1343] "ENSMUSG00000115372.1" "ENSMUSG00000048100.13"
## [1345] "ENSMUSG00000040659.3" "ENSMUSG00000064307.13"
## [1347] "ENSMUSG00000115896.1" "ENSMUSG00000117497.1"
## [1349] "ENSMUSG00000052738.14" "ENSMUSG00000052403.11"
## [1351] "ENSMUSG00000113179.1" "ENSMUSG00000046367.10"
## [1353] "ENSMUSG00000039841.14" "ENSMUSG00000095296.7"
## [1355] "ENSMUSG00000015335.16" "ENSMUSG00000051695.6"
## [1357] "ENSMUSG00000024076.10" "ENSMUSG00000021101.2"
## [1359] "ENSMUSG00000109293.1" "ENSMUSG00000025257.5"
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## [1363] "ENSMUSG00000021620.4" "ENSMUSG00000028657.14"
## [1365] "ENSMUSG00000074656.12" "ENSMUSG00000038416.15"
## [1367] "ENSMUSG00000099354.6" "ENSMUSG00000047446.18"
## [1369] "ENSMUSG00000019888.16" "ENSMUSG00000105651.1"
## [1371] "ENSMUSG00000057113.13" "ENSMUSG00000055547.4"
## [1373] "ENSMUSG00000118339.1" "ENSMUSG00000048516.2"
## [1375] "ENSMUSG00000039477.16" "ENSMUSG00000017716.15"
## [1377] "ENSMUSG00000114333.1" "ENSMUSG00000022322.8"
## [1379] "ENSMUSG00000031754.10" "ENSMUSG00000011486.14"
## [1381] "ENSMUSG00000028337.14" "ENSMUSG00000015443.9"
## [1383] "ENSMUSG00000107144.1" "ENSMUSG00000074634.12"
## [1385] "ENSMUSG00000031762.7" "ENSMUSG00000028945.9"
## [1387] "ENSMUSG00000028560.11" "ENSMUSG00000061392.2"
## [1389] "ENSMUSG00000049902.6" "ENSMUSG00000029552.19"
## [1391] "ENSMUSG00000083012.9" "ENSMUSG00000037661.14"
## [1393] "ENSMUSG00000024175.2" "ENSMUSG00000030096.8"
## [1395] "ENSMUSG00000022681.15" "ENSMUSG00000037913.12"
## [1397] "ENSMUSG00000034544.17" "ENSMUSG00000050526.5"
## [1399] "ENSMUSG00000009291.13" "ENSMUSG00000115774.1"
## [1401] "ENSMUSG00000021846.9" "ENSMUSG00000031453.16"
## [1403] "ENSMUSG00000095979.7" "ENSMUSG00000085725.2"
## [1405] "ENSMUSG00000021892.14" "ENSMUSG00000027203.15"
## [1407] "ENSMUSG00000031845.15" "ENSMUSG00000021056.8"
## [1409] "ENSMUSG00000037910.2" "ENSMUSG00000020212.14"
## [1411] "ENSMUSG00000045587.9" "ENSMUSG00000028630.9"
## [1413] "ENSMUSG00000026142.15" "ENSMUSG00000073976.10"
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## [1465] "ENSMUSG00000005802.12" "ENSMUSG00000110275.1"
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## [1483] "ENSMUSG00000115177.1" "ENSMUSG00000030345.16"
## [1485] "ENSMUSG00000099751.6" "ENSMUSG00000029634.15"
## [1487] "ENSMUSG00000084811.2" "ENSMUSG00000022855.9"
## [1489] "ENSMUSG00000076438.5" "ENSMUSG00000026484.13"
## [1491] "ENSMUSG00000051804.3" "ENSMUSG00000027787.14"
## [1493] "ENSMUSG00000047046.8" "ENSMUSG00000097717.2"
## [1495] "ENSMUSG00000033323.14" "ENSMUSG00000031927.9"
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## [1503] "ENSMUSG00000113210.1" "ENSMUSG00000054091.9"
## [1505] "ENSMUSG00000022116.7" "ENSMUSG00000032239.10"
## [1507] "ENSMUSG00000029186.12" "ENSMUSG00000002031.13"
## [1509] "ENSMUSG00000056537.11" "ENSMUSG00000095324.2"
## [1511] "ENSMUSG00000078941.9" "ENSMUSG00000022428.8"
## [1513] "ENSMUSG00000055862.7" "ENSMUSG00000029681.12"
## [1515] "ENSMUSG00000107031.1" "ENSMUSG00000035491.5"
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## [1519] "ENSMUSG00000020213.6" "ENSMUSG00000030877.11"
## [1521] "ENSMUSG00000034371.9" "ENSMUSG00000086327.2"
## [1523] "ENSMUSG00000028809.16" "ENSMUSG00000086954.1"
## [1525] "ENSMUSG00000078139.3" "ENSMUSG00000074063.10"
## [1527] "ENSMUSG00000051234.6" "ENSMUSG00000002372.9"
## [1529] "ENSMUSG00000099735.1" "ENSMUSG00000043460.7"
## [1531] "ENSMUSG00000009647.13" "ENSMUSG00000050628.6"
## [1533] "ENSMUSG00000116547.1" "ENSMUSG00000015542.17"
## [1535] "ENSMUSG00000043535.13" "ENSMUSG00000021610.8"
## [1537] "ENSMUSG00000086277.2" "ENSMUSG00000020780.15"
## [1539] "ENSMUSG00000011350.15" "ENSMUSG00000032021.14"
## [1541] "ENSMUSG00000069049.11" "ENSMUSG00000015095.12"
## [1543] "ENSMUSG00000087526.2" "ENSMUSG00000022285.17"
## [1545] "ENSMUSG00000020660.6" "ENSMUSG00000044468.14"
## [1547] "ENSMUSG00000015961.8" "ENSMUSG00000112337.1"
## [1549] "ENSMUSG00000072188.4" "ENSMUSG00000114879.1"
## [1551] "ENSMUSG00000095829.8" "ENSMUSG00000038057.4"
## [1553] "ENSMUSG00000094021.7" "ENSMUSG00000021792.15"
## [1555] "ENSMUSG00000072647.6" "ENSMUSG00000030089.15"
## [1557] "ENSMUSG00000032611.9" "ENSMUSG00000021916.16"
## [1559] "ENSMUSG00000056515.9" "ENSMUSG00000040367.2"
## [1561] "ENSMUSG00000022685.9" "ENSMUSG00000025050.8"
## [1563] "ENSMUSG00000027404.15" "ENSMUSG00000093568.1"
## [1565] "ENSMUSG00000079407.9" "ENSMUSG00000024695.16"
## [1567] "ENSMUSG00000048481.15" "ENSMUSG00000050150.16"
## [1569] "ENSMUSG00000118047.1" "ENSMUSG00000018882.12"
## [1571] "ENSMUSG00000097962.7" "ENSMUSG00000099722.3"
## [1573] "ENSMUSG00000032187.16" "ENSMUSG00000021103.12"
## [1575] "ENSMUSG00000078129.2" "ENSMUSG00000024400.16"
## [1577] "ENSMUSG00000048626.5" "ENSMUSG00000039218.17"
## [1579] "ENSMUSG00000022035.6" "ENSMUSG00000049653.5"
## [1581] "ENSMUSG00000079091.1" "ENSMUSG00000054383.2"
## [1583] "ENSMUSG00000019808.8" "ENSMUSG00000024926.10"
## [1585] "ENSMUSG00000021879.13" "ENSMUSG00000029388.14"
## [1587] "ENSMUSG00000111830.1" "ENSMUSG00000020372.15"
## [1589] "ENSMUSG00000084998.1" "ENSMUSG00000051223.14"
## [1591] "ENSMUSG00000070544.6" "ENSMUSG00000025137.15"
## [1593] "ENSMUSG00000029660.10" "ENSMUSG00000022314.10"
## [1595] "ENSMUSG00000115335.1" "ENSMUSG00000099794.1"
## [1597] "ENSMUSG00000039176.17" "ENSMUSG00000031516.11"
## [1599] "ENSMUSG00000047804.15" "ENSMUSG00000022388.14"
## [1601] "ENSMUSG00000037638.5" "ENSMUSG00000022185.19"
## [1603] "ENSMUSG00000046886.6" "ENSMUSG00000044306.4"
## [1605] "ENSMUSG00000021221.15" "ENSMUSG00000030980.17"
## [1607] "ENSMUSG00000100175.6" "ENSMUSG00000105340.5"
## [1609] "ENSMUSG00000027357.16" "ENSMUSG00000045896.14"
## [1611] "ENSMUSG00000100911.2" "ENSMUSG00000079707.10"
## [1613] "ENSMUSG00000111712.1" "ENSMUSG00000021622.3"
## [1615] "ENSMUSG00000066152.11" "ENSMUSG00000005103.12"
## [1617] "ENSMUSG00000109858.1" "ENSMUSG00000019834.15"
## [1619] "ENSMUSG00000047407.17" "ENSMUSG00000026255.15"
## [1621] "ENSMUSG00000063568.11" "ENSMUSG00000090012.1"
## [1623] "ENSMUSG00000004270.13" "ENSMUSG00000026554.15"
## [1625] "ENSMUSG00000032042.11" "ENSMUSG00000038646.13"
## [1627] "ENSMUSG00000005823.9" "ENSMUSG00000096732.7"
## [1629] "ENSMUSG00000035614.11" "ENSMUSG00000032026.7"
## [1631] "ENSMUSG00000053730.15" "ENSMUSG00000036572.16"
## [1633] "ENSMUSG00000045328.11" "ENSMUSG00000110310.1"
## [1635] "ENSMUSG00000019297.9" "ENSMUSG00000023403.14"
## [1637] "ENSMUSG00000039342.5" "ENSMUSG00000014351.12"
## [1639] "ENSMUSG00000054160.2" "ENSMUSG00000028688.13"
## [1641] "ENSMUSG00000053040.13" "ENSMUSG00000084984.8"
## [1643] "ENSMUSG00000116585.1" "ENSMUSG00000015176.11"
## [1645] "ENSMUSG00000107164.1" "ENSMUSG00000048602.9"
## [1647] "ENSMUSG00000029168.14" "ENSMUSG00000046958.10"
## [1649] "ENSMUSG00000091803.7" "ENSMUSG00000074807.3"
## [1651] "ENSMUSG00000055093.10" "ENSMUSG00000116970.1"
## [1653] "ENSMUSG00000090118.1" "ENSMUSG00000027469.16"
## [1655] "ENSMUSG00000029474.7" "ENSMUSG00000064129.4"
## [1657] "ENSMUSG00000049932.3" "ENSMUSG00000101314.1"
## [1659] "ENSMUSG00000062604.11" "ENSMUSG00000059042.3"
## [1661] "ENSMUSG00000040163.14" "ENSMUSG00000030611.10"
## [1663] "ENSMUSG00000112785.1" "ENSMUSG00000041716.7"
## [1665] "ENSMUSG00000091122.8" "ENSMUSG00000004934.14"
## [1667] "ENSMUSG00000025134.2" "ENSMUSG00000115286.1"
## [1669] "ENSMUSG00000100075.1" "ENSMUSG00000048174.2"
## [1671] "ENSMUSG00000038909.16" "ENSMUSG00000020455.16"
## [1673] "ENSMUSG00000022683.13" "ENSMUSG00000036918.16"
## [1675] "ENSMUSG00000030922.12" "ENSMUSG00000087544.1"
## [1677] "ENSMUSG00000090764.8" "ENSMUSG00000025288.1"
## [1679] "ENSMUSG00000110717.1" "ENSMUSG00000070520.4"
## [1681] "ENSMUSG00000079702.5" "ENSMUSG00000086080.7"
## [1683] "ENSMUSG00000113087.1" "ENSMUSG00000017286.15"
## [1685] "ENSMUSG00000026039.9" "ENSMUSG00000075571.8"
## [1687] "ENSMUSG00000037253.8" "ENSMUSG00000021500.17"
## [1689] "ENSMUSG00000028284.13" "ENSMUSG00000027236.8"
## [1691] "ENSMUSG00000063900.5" "ENSMUSG00000073725.8"
## [1693] "ENSMUSG00000055148.7" "ENSMUSG00000085614.1"
## [1695] "ENSMUSG00000098127.1" "ENSMUSG00000030138.8"
## [1697] "ENSMUSG00000028409.11" "ENSMUSG00000069972.6"
## [1699] "ENSMUSG00000040600.9" "ENSMUSG00000005763.15"
## [1701] "ENSMUSG00000086112.1" "ENSMUSG00000025762.15"
## [1703] "ENSMUSG00000029657.15" "ENSMUSG00000053719.10"
## [1705] "ENSMUSG00000025873.16" "ENSMUSG00000099872.1"
## [1707] "ENSMUSG00000031479.9" "ENSMUSG00000085240.1"
## [1709] "ENSMUSG00000099384.6" "ENSMUSG00000030623.4"
## [1711] "ENSMUSG00000078126.4" "ENSMUSG00000079532.1"
## [1713] "ENSMUSG00000027255.14" "ENSMUSG00000110929.1"
## [1715] "ENSMUSG00000040359.14" "ENSMUSG00000036955.16"
## [1717] "ENSMUSG00000031609.3" "ENSMUSG00000039632.13"
## [1719] "ENSMUSG00000046723.4" "ENSMUSG00000062203.15"
## [1721] "ENSMUSG00000071172.13" "ENSMUSG00000031429.14"
## [1723] "ENSMUSG00000035454.1" "ENSMUSG00000027620.16"
## [1725] "ENSMUSG00000041703.7" "ENSMUSG00000028522.16"
## [1727] "ENSMUSG00000095028.6" "ENSMUSG00000020513.15"
## [1729] "ENSMUSG00000037247.3" "ENSMUSG00000099853.3"
## [1731] "ENSMUSG00000024335.20" "ENSMUSG00000104872.1"
## [1733] "ENSMUSG00000100133.1" "ENSMUSG00000028333.10"
## [1735] "ENSMUSG00000037279.13" "ENSMUSG00000109986.1"
## [1737] "ENSMUSG00000052833.9" "ENSMUSG00000096828.2"
## [1739] "ENSMUSG00000021759.14" "ENSMUSG00000061451.13"
## [1741] "ENSMUSG00000041645.14" "ENSMUSG00000028277.13"
## [1743] "ENSMUSG00000057554.13" "ENSMUSG00000087574.1"
## [1745] "ENSMUSG00000038170.15" "ENSMUSG00000068039.13"
## [1747] "ENSMUSG00000090386.10" "ENSMUSG00000074825.4"
## [1749] "ENSMUSG00000031158.11" "ENSMUSG00000081638.4"
## [1751] "ENSMUSG00000108627.1" "ENSMUSG00000002324.8"
## [1753] "ENSMUSG00000048755.9" "ENSMUSG00000032218.7"
## [1755] "ENSMUSG00000034563.16" "ENSMUSG00000048406.5"
## [1757] "ENSMUSG00000024687.11" "ENSMUSG00000099662.1"
## [1759] "ENSMUSG00000045466.18" "ENSMUSG00000099630.1"
## [1761] "ENSMUSG00000079701.7" "ENSMUSG00000025373.14"
## [1763] "ENSMUSG00000061167.9" "ENSMUSG00000021758.14"
## [1765] "ENSMUSG00000024207.8" "ENSMUSG00000032869.15"
## [1767] "ENSMUSG00000073267.5" "ENSMUSG00000029725.10"
## [1769] "ENSMUSG00000030549.6" "ENSMUSG00000102122.1"
## [1771] "ENSMUSG00000095807.2" "ENSMUSG00000026526.14"
## [1773] "ENSMUSG00000028799.15" "ENSMUSG00000003123.15"
## [1775] "ENSMUSG00000100856.1" "ENSMUSG00000101189.1"
## [1777] "ENSMUSG00000021993.10" "ENSMUSG00000100668.1"
## [1779] "ENSMUSG00000116491.1" "ENSMUSG00000084859.7"
## [1781] "ENSMUSG00000064345.1" "ENSMUSG00000105978.1"
## [1783] "ENSMUSG00000022039.6" "ENSMUSG00000091933.2"
## [1785] "ENSMUSG00000090258.7" "ENSMUSG00000029138.4"
## [1787] "ENSMUSG00000034327.17" "ENSMUSG00000059237.6"
## [1789] "ENSMUSG00000030224.10" "ENSMUSG00000037710.8"
## [1791] "ENSMUSG00000031166.13" "ENSMUSG00000085616.1"
## [1793] "ENSMUSG00000034377.10" "ENSMUSG00000001120.15"
## [1795] "ENSMUSG00000018736.14" "ENSMUSG00000112611.1"
## [1797] "ENSMUSG00000020268.14" "ENSMUSG00000086134.1"
## [1799] "ENSMUSG00000030214.7" "ENSMUSG00000005131.4"
## [1801] "ENSMUSG00000052033.13" "ENSMUSG00000014313.15"
## [1803] "ENSMUSG00000099508.1" "ENSMUSG00000055159.7"
## [1805] "ENSMUSG00000025484.9" "ENSMUSG00000024826.15"
## [1807] "ENSMUSG00000115450.1" "ENSMUSG00000027001.10"
## [1809] "ENSMUSG00000098144.8" "ENSMUSG00000045983.16"
## [1811] "ENSMUSG00000062456.4" "ENSMUSG00000014767.17"
## [1813] "ENSMUSG00000085418.1" "ENSMUSG00000047515.8"
## [1815] "ENSMUSG00000115245.1" "ENSMUSG00000028998.6"
## [1817] "ENSMUSG00000045107.5" "ENSMUSG00000008429.8"
## [1819] "ENSMUSG00000020570.15" "ENSMUSG00000090585.8"
## [1821] "ENSMUSG00000034303.7" "ENSMUSG00000086186.1"
## [1823] "ENSMUSG00000110629.1" "ENSMUSG00000021810.3"
## [1825] "ENSMUSG00000063972.13" "ENSMUSG00000053453.9"
## [1827] "ENSMUSG00000108354.1" "ENSMUSG00000005982.14"
## [1829] "ENSMUSG00000020669.15" "ENSMUSG00000029402.8"
## [1831] "ENSMUSG00000009079.16" "ENSMUSG00000021338.17"
## [1833] "ENSMUSG00000031843.2" "ENSMUSG00000022269.13"
## [1835] "ENSMUSG00000099792.1" "ENSMUSG00000013858.14"
## [1837] "ENSMUSG00000032802.8" "ENSMUSG00000027927.5"
## [1839] "ENSMUSG00000048520.16" "ENSMUSG00000078087.5"
## [1841] "ENSMUSG00000089914.2" "ENSMUSG00000037822.12"
## [1843] "ENSMUSG00000030291.12" "ENSMUSG00000054727.2"
## [1845] "ENSMUSG00000030741.15" "ENSMUSG00000054362.9"
## [1847] "ENSMUSG00000028251.5" "ENSMUSG00000027613.15"
## [1849] "ENSMUSG00000060376.7" "ENSMUSG00000001018.15"
## [1851] "ENSMUSG00000026754.16" "ENSMUSG00000022052.9"
## [1853] "ENSMUSG00000031637.13" "ENSMUSG00000105297.1"
## [1855] "ENSMUSG00000038534.18" "ENSMUSG00000018509.8"
## [1857] "ENSMUSG00000040731.13" "ENSMUSG00000112484.1"
## [1859] "ENSMUSG00000084875.2" "ENSMUSG00000027379.13"
## [1861] "ENSMUSG00000024660.9" "ENSMUSG00000066324.2"
## [1863] "ENSMUSG00000054391.12" "ENSMUSG00000035057.7"
## [1865] "ENSMUSG00000048911.15" "ENSMUSG00000020973.7"
## [1867] "ENSMUSG00000085247.1" "ENSMUSG00000097127.7"
## [1869] "ENSMUSG00000043015.15" "ENSMUSG00000037720.16"
## [1871] "ENSMUSG00000067028.11" "ENSMUSG00000005609.16"
## [1873] "ENSMUSG00000079005.3" "ENSMUSG00000051518.8"
## [1875] "ENSMUSG00000115139.1" "ENSMUSG00000106938.1"
## [1877] "ENSMUSG00000086816.1" "ENSMUSG00000022748.8"
## [1879] "ENSMUSG00000020895.14" "ENSMUSG00000002205.16"
## [1881] "ENSMUSG00000021615.13" "ENSMUSG00000038498.4"
## [1883] "ENSMUSG00000087363.1" "ENSMUSG00000036822.6"
## [1885] "ENSMUSG00000075070.6" "ENSMUSG00000020077.14"
## [1887] "ENSMUSG00000058586.12" "ENSMUSG00000096914.3"
## [1889] "ENSMUSG00000104529.4" "ENSMUSG00000045391.4"
## [1891] "ENSMUSG00000022369.13" "ENSMUSG00000111639.1"
## [1893] "ENSMUSG00000002190.13" "ENSMUSG00000021890.6"
## [1895] "ENSMUSG00000029094.12" "ENSMUSG00000078919.10"
## [1897] "ENSMUSG00000093617.1" "ENSMUSG00000032666.16"
## [1899] "ENSMUSG00000062438.4" "ENSMUSG00000078652.9"
## [1901] "ENSMUSG00000021196.14" "ENSMUSG00000032254.10"
## [1903] "ENSMUSG00000110343.1" "ENSMUSG00000102045.1"
## [1905] "ENSMUSG00000061887.14" "ENSMUSG00000027018.11"
## [1907] "ENSMUSG00000048701.13" "ENSMUSG00000099681.1"
## [1909] "ENSMUSG00000029517.13" "ENSMUSG00000086817.1"
## [1911] "ENSMUSG00000040714.14" "ENSMUSG00000022710.17"
## [1913] "ENSMUSG00000043415.5" "ENSMUSG00000114334.1"
## [1915] "ENSMUSG00000031996.17" "ENSMUSG00000022103.10"
## [1917] "ENSMUSG00000026646.16" "ENSMUSG00000091970.3"
## [1919] "ENSMUSG00000115284.1" "ENSMUSG00000032966.14"
## [1921] "ENSMUSG00000052273.4" "ENSMUSG00000020993.9"
## [1923] "ENSMUSG00000085100.1" "ENSMUSG00000021997.4"
## [1925] "ENSMUSG00000075524.3" "ENSMUSG00000032232.14"
## [1927] "ENSMUSG00000093383.1" "ENSMUSG00000033671.18"
## [1929] "ENSMUSG00000036411.10" "ENSMUSG00000020974.6"
## [1931] "ENSMUSG00000097841.2" "ENSMUSG00000083380.1"
## [1933] "ENSMUSG00000090063.6" "ENSMUSG00000107305.1"
## [1935] "ENSMUSG00000038453.17" "ENSMUSG00000029504.5"
## [1937] "ENSMUSG00000118491.1" "ENSMUSG00000049692.7"
## [1939] "ENSMUSG00000026643.16" "ENSMUSG00000021671.9"
## [1941] "ENSMUSG00000028567.8" "ENSMUSG00000106549.1"
## [1943] "ENSMUSG00000021086.5" "ENSMUSG00000050912.15"
## [1945] "ENSMUSG00000095785.2" "ENSMUSG00000117000.1"
## [1947] "ENSMUSG00000020612.16" "ENSMUSG00000090713.2"
## [1949] "ENSMUSG00000027306.15" "ENSMUSG00000029875.5"
## [1951] "ENSMUSG00000056383.10" "ENSMUSG00000026882.1"
## [1953] "ENSMUSG00000037443.13" "ENSMUSG00000101634.6"
## [1955] "ENSMUSG00000027823.9" "ENSMUSG00000023075.9"
## [1957] "ENSMUSG00000028447.11" "ENSMUSG00000027940.18"
## [1959] "ENSMUSG00000070372.11" "ENSMUSG00000024259.9"
## [1961] "ENSMUSG00000106876.1" "ENSMUSG00000027131.3"
## [1963] "ENSMUSG00000107895.1" "ENSMUSG00000106918.3"
## [1965] "ENSMUSG00000020986.13" "ENSMUSG00000038374.10"
## [1967] "ENSMUSG00000042688.16" "ENSMUSG00000040822.7"
## [1969] "ENSMUSG00000095452.2" "ENSMUSG00000090379.1"
## [1971] "ENSMUSG00000067038.6" "ENSMUSG00000055762.16"
## [1973] "ENSMUSG00000030590.15" "ENSMUSG00000087258.1"
## [1975] "ENSMUSG00000020576.10" "ENSMUSG00000046229.10"
## [1977] "ENSMUSG00000033953.10" "ENSMUSG00000037972.7"
## [1979] "ENSMUSG00000057110.15" "ENSMUSG00000022555.12"
## [1981] "ENSMUSG00000026941.16" "ENSMUSG00000010376.15"
## [1983] "ENSMUSG00000096901.7" "ENSMUSG00000029131.14"
## [1985] "ENSMUSG00000060407.6" "ENSMUSG00000049295.17"
## [1987] "ENSMUSG00000078935.1" "ENSMUSG00000075232.6"
## [1989] "ENSMUSG00000022111.9" "ENSMUSG00000030264.14"
## [1991] "ENSMUSG00000085044.1" "ENSMUSG00000037364.12"
## [1993] "ENSMUSG00000020463.15" "ENSMUSG00000029707.6"
## [1995] "ENSMUSG00000111028.1" "ENSMUSG00000019878.8"
## [1997] "ENSMUSG00000022965.8" "ENSMUSG00000085759.1"
## [1999] "ENSMUSG00000087185.1" "ENSMUSG00000086732.1"
##
##
## $summary
## $summary$n_features
## [1] 2000
##
## $summary$n_cells
## [1] 300
##
##
## $results
## class: SingleCellExperiment
## dim: 2000 300
## metadata(4): neighbors velocity_params velocity_graph
## velocity_graph_neg
## assays(6): X spliced ... Mu velocity
## rownames(2000): ENSMUSG00000117819.1
## ENSMUSG00000081984.3 ... ENSMUSG00000087185.1
## ENSMUSG00000086732.1
## rowData names(4): velocity_gamma velocity_qreg_ratio
## velocity_r2 velocity_genes
## colnames(300): CCCATACTCCGAAGAG AATCCAGTCATCTGCC ...
## GCGCGATAGGCTCATT CTAAGACTCACTATTC
## colData names(7): velocity_self_transition root_cells
## ... velocity_confidence
## velocity_confidence_transition## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## reducedDimNames(1): X_pca
## mainExpName: NULL## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## altExpNames(0):
##
## $reductions
## character(0)
##
## $coldata_fields
## [1] "velocity_pseudotime" "velocity_confidence"
## [3] "root_cells" "end_points"
##
## $created_at
## [1] "2026-07-05 20:46:46 UTC"
##
## $mode
## [1] "deterministic"
##
## $use.dimred
## [1] "PCA"
##
## $subset.row
## [1] "ENSMUSG00000117819.1" "ENSMUSG00000081984.3"
## [3] "ENSMUSG00000047995.7" "ENSMUSG00000060860.8"
## [5] "ENSMUSG00000100153.2" "ENSMUSG00000090137.8"
## [7] "ENSMUSG00000064220.6" "ENSMUSG00000064351.1"
## [9] "ENSMUSG00000063954.7" "ENSMUSG00000027505.2"
## [11] "ENSMUSG00000059695.4" "ENSMUSG00000038994.6"
## [13] "ENSMUSG00000027431.5" "ENSMUSG00000018543.8"
## [15] "ENSMUSG00000105734.1" "ENSMUSG00000042800.5"
## [17] "ENSMUSG00000022832.11" "ENSMUSG00000048686.4"
## [19] "ENSMUSG00000100937.1" "ENSMUSG00000028259.13"
## [21] "ENSMUSG00000030976.3" "ENSMUSG00000079710.10"
## [23] "ENSMUSG00000020483.14" "ENSMUSG00000094624.1"
## [25] "ENSMUSG00000031512.15" "ENSMUSG00000078577.3"
## [27] "ENSMUSG00000078554.2" "ENSMUSG00000048077.6"
## [29] "ENSMUSG00000008482.9" "ENSMUSG00000079666.8"
## [31] "ENSMUSG00000041399.3" "ENSMUSG00000029867.5"
## [33] "ENSMUSG00000027564.4" "ENSMUSG00000070708.5"
## [35] "ENSMUSG00000050621.7" "ENSMUSG00000031991.10"
## [37] "ENSMUSG00000009093.7" "ENSMUSG00000047129.11"
## [39] "ENSMUSG00000085861.1" "ENSMUSG00000025482.11"
## [41] "ENSMUSG00000020286.12" "ENSMUSG00000062154.14"
## [43] "ENSMUSG00000050058.6" "ENSMUSG00000095384.1"
## [45] "ENSMUSG00000051276.4" "ENSMUSG00000045521.7"
## [47] "ENSMUSG00000028264.16" "ENSMUSG00000029723.16"
## [49] "ENSMUSG00000053184.15" "ENSMUSG00000118396.2"
## [51] "ENSMUSG00000021838.17" "ENSMUSG00000029433.16"
## [53] "ENSMUSG00000047841.8" "ENSMUSG00000057072.11"
## [55] "ENSMUSG00000066383.7" "ENSMUSG00000062028.8"
## [57] "ENSMUSG00000044444.6" "ENSMUSG00000047843.16"
## [59] "ENSMUSG00000079346.4" "ENSMUSG00000027938.11"
## [61] "ENSMUSG00000063971.7" "ENSMUSG00000041673.12"
## [63] "ENSMUSG00000045709.11" "ENSMUSG00000028938.9"
## [65] "ENSMUSG00000101959.1" "ENSMUSG00000099863.1"
## [67] "ENSMUSG00000032900.15" "ENSMUSG00000027442.10"
## [69] "ENSMUSG00000038691.5" "ENSMUSG00000064357.1"
## [71] "ENSMUSG00000046755.5" "ENSMUSG00000024233.10"
## [73] "ENSMUSG00000008393.9" "ENSMUSG00000020617.13"
## [75] "ENSMUSG00000044526.3" "ENSMUSG00000020945.13"
## [77] "ENSMUSG00000043629.12" "ENSMUSG00000074748.3"
## [79] "ENSMUSG00000066500.5" "ENSMUSG00000049916.12"
## [81] "ENSMUSG00000032803.15" "ENSMUSG00000068240.5"
## [83] "ENSMUSG00000055826.5" "ENSMUSG00000038523.10"
## [85] "ENSMUSG00000059455.3" "ENSMUSG00000048731.15"
## [87] "ENSMUSG00000044056.3" "ENSMUSG00000024430.14"
## [89] "ENSMUSG00000051113.9" "ENSMUSG00000095040.2"
## [91] "ENSMUSG00000030714.14" "ENSMUSG00000070489.5"
## [93] "ENSMUSG00000030859.8" "ENSMUSG00000022148.16"
## [95] "ENSMUSG00000053375.8" "ENSMUSG00000041566.3"
## [97] "ENSMUSG00000064358.1" "ENSMUSG00000061477.4"
## [99] "ENSMUSG00000100282.1" "ENSMUSG00000036438.14"
## [101] "ENSMUSG00000067909.4" "ENSMUSG00000021545.5"
## [103] "ENSMUSG00000054523.13" "ENSMUSG00000031682.5"
## [105] "ENSMUSG00000045942.13" "ENSMUSG00000090117.7"
## [107] "ENSMUSG00000037307.11" "ENSMUSG00000050685.5"
## [109] "ENSMUSG00000038709.14" "ENSMUSG00000014301.13"
## [111] "ENSMUSG00000024501.20" "ENSMUSG00000037708.16"
## [113] "ENSMUSG00000059288.14" "ENSMUSG00000064341.1"
## [115] "ENSMUSG00000100862.1" "ENSMUSG00000027674.16"
## [117] "ENSMUSG00000027355.15" "ENSMUSG00000074344.7"
## [119] "ENSMUSG00000073758.10" "ENSMUSG00000027886.7"
## [121] "ENSMUSG00000070563.6" "ENSMUSG00000055553.16"
## [123] "ENSMUSG00000026963.4" "ENSMUSG00000021768.15"
## [125] "ENSMUSG00000101111.1" "ENSMUSG00000041540.16"
## [127] "ENSMUSG00000030858.10" "ENSMUSG00000005803.14"
## [129] "ENSMUSG00000109864.1" "ENSMUSG00000056509.10"
## [131] "ENSMUSG00000091396.2" "ENSMUSG00000047150.8"
## [133] "ENSMUSG00000074435.10" "ENSMUSG00000069971.5"
## [135] "ENSMUSG00000089989.10" "ENSMUSG00000010435.7"
## [137] "ENSMUSG00000037689.6" "ENSMUSG00000027606.12"
## [139] "ENSMUSG00000029477.14" "ENSMUSG00000026592.13"
## [141] "ENSMUSG00000058935.14" "ENSMUSG00000035085.5"
## [143] "ENSMUSG00000060491.14" "ENSMUSG00000095159.2"
## [145] "ENSMUSG00000026809.15" "ENSMUSG00000095869.1"
## [147] "ENSMUSG00000049154.12" "ENSMUSG00000048655.17"
## [149] "ENSMUSG00000046173.3" "ENSMUSG00000021961.6"
## [151] "ENSMUSG00000026864.13" "ENSMUSG00000095789.6"
## [153] "ENSMUSG00000045336.5" "ENSMUSG00000020234.10"
## [155] "ENSMUSG00000001558.5" "ENSMUSG00000031452.15"
## [157] "ENSMUSG00000055692.21" "ENSMUSG00000023467.18"
## [159] "ENSMUSG00000026827.12" "ENSMUSG00000050141.13"
## [161] "ENSMUSG00000043050.8" "ENSMUSG00000021415.13"
## [163] "ENSMUSG00000019876.15" "ENSMUSG00000063480.8"
## [165] "ENSMUSG00000036924.3" "ENSMUSG00000052920.16"
## [167] "ENSMUSG00000013091.5" "ENSMUSG00000086361.1"
## [169] "ENSMUSG00000073380.2" "ENSMUSG00000049761.6"
## [171] "ENSMUSG00000033949.12" "ENSMUSG00000116210.1"
## [173] "ENSMUSG00000073731.12" "ENSMUSG00000047025.5"
## [175] "ENSMUSG00000030161.8" "ENSMUSG00000040883.18"
## [177] "ENSMUSG00000006941.5" "ENSMUSG00000072772.3"
## [179] "ENSMUSG00000041791.6" "ENSMUSG00000100684.1"
## [181] "ENSMUSG00000043633.6" "ENSMUSG00000027496.15"
## [183] "ENSMUSG00000047518.3" "ENSMUSG00000048573.9"
## [185] "ENSMUSG00000023257.3" "ENSMUSG00000064354.1"
## [187] "ENSMUSG00000078127.3" "ENSMUSG00000090840.2"
## [189] "ENSMUSG00000022249.14" "ENSMUSG00000020460.15"
## [191] "ENSMUSG00000095867.2" "ENSMUSG00000043859.5"
## [193] "ENSMUSG00000028141.11" "ENSMUSG00000110464.1"
## [195] "ENSMUSG00000059430.14" "ENSMUSG00000047108.4"
## [197] "ENSMUSG00000021585.10" "ENSMUSG00000020270.9"
## [199] "ENSMUSG00000101796.1" "ENSMUSG00000049694.13"
## [201] "ENSMUSG00000026969.3" "ENSMUSG00000024397.14"
## [203] "ENSMUSG00000026182.6" "ENSMUSG00000034913.10"
## [205] "ENSMUSG00000061474.11" "ENSMUSG00000044122.15"
## [207] "ENSMUSG00000028575.11" "ENSMUSG00000021534.8"
## [209] "ENSMUSG00000117852.1" "ENSMUSG00000030421.9"
## [211] "ENSMUSG00000036167.16" "ENSMUSG00000039555.14"
## [213] "ENSMUSG00000017767.3" "ENSMUSG00000009115.5"
## [215] "ENSMUSG00000036244.5" "ENSMUSG00000035522.3"
## [217] "ENSMUSG00000008307.11" "ENSMUSG00000026226.16"
## [219] "ENSMUSG00000050641.7" "ENSMUSG00000102070.1"
## [221] "ENSMUSG00000028427.13" "ENSMUSG00000032530.14"
## [223] "ENSMUSG00000048206.6" "ENSMUSG00000061633.3"
## [225] "ENSMUSG00000007907.4" "ENSMUSG00000004633.17"
## [227] "ENSMUSG00000046957.5" "ENSMUSG00000022501.6"
## [229] "ENSMUSG00000027480.12" "ENSMUSG00000030629.15"
## [231] "ENSMUSG00000020622.17" "ENSMUSG00000089781.2"
## [233] "ENSMUSG00000040541.8" "ENSMUSG00000026940.3"
## [235] "ENSMUSG00000099353.7" "ENSMUSG00000046750.17"
## [237] "ENSMUSG00000021203.15" "ENSMUSG00000070999.2"
## [239] "ENSMUSG00000062651.4" "ENSMUSG00000033213.16"
## [241] "ENSMUSG00000101894.1" "ENSMUSG00000045378.5"
## [243] "ENSMUSG00000020940.13" "ENSMUSG00000090202.1"
## [245] "ENSMUSG00000002240.12" "ENSMUSG00000031509.10"
## [247] "ENSMUSG00000019945.10" "ENSMUSG00000030344.11"
## [249] "ENSMUSG00000038015.6" "ENSMUSG00000038180.11"
## [251] "ENSMUSG00000070332.4" "ENSMUSG00000067367.9"
## [253] "ENSMUSG00000017720.2" "ENSMUSG00000097522.1"
## [255] "ENSMUSG00000012405.16" "ENSMUSG00000085940.1"
## [257] "ENSMUSG00000032110.4" "ENSMUSG00000090273.3"
## [259] "ENSMUSG00000078161.8" "ENSMUSG00000001175.15"
## [261] "ENSMUSG00000048994.2" "ENSMUSG00000058173.12"
## [263] "ENSMUSG00000007591.15" "ENSMUSG00000024059.10"
## [265] "ENSMUSG00000055891.7" "ENSMUSG00000004455.16"
## [267] "ENSMUSG00000050089.13" "ENSMUSG00000066878.5"
## [269] "ENSMUSG00000041068.6" "ENSMUSG00000038997.4"
## [271] "ENSMUSG00000030206.13" "ENSMUSG00000070392.5"
## [273] "ENSMUSG00000028332.13" "ENSMUSG00000062867.13"
## [275] "ENSMUSG00000043036.13" "ENSMUSG00000116615.1"
## [277] "ENSMUSG00000029678.8" "ENSMUSG00000002308.16"
## [279] "ENSMUSG00000003518.13" "ENSMUSG00000062825.15"
## [281] "ENSMUSG00000020096.20" "ENSMUSG00000089743.7"
## [283] "ENSMUSG00000028484.16" "ENSMUSG00000030385.4"
## [285] "ENSMUSG00000029909.6" "ENSMUSG00000026931.10"
## [287] "ENSMUSG00000030077.11" "ENSMUSG00000021499.12"
## [289] "ENSMUSG00000058690.14" "ENSMUSG00000090206.8"
## [291] "ENSMUSG00000045004.3" "ENSMUSG00000022982.10"
## [293] "ENSMUSG00000070979.5" "ENSMUSG00000040681.16"
## [295] "ENSMUSG00000094975.1" "ENSMUSG00000014529.9"
## [297] "ENSMUSG00000062075.13" "ENSMUSG00000021590.7"
## [299] "ENSMUSG00000040456.2" "ENSMUSG00000029682.5"
## [301] "ENSMUSG00000022674.15" "ENSMUSG00000022993.7"
## [303] "ENSMUSG00000020636.14" "ENSMUSG00000097638.1"
## [305] "ENSMUSG00000029607.14" "ENSMUSG00000093394.1"
## [307] "ENSMUSG00000045022.6" "ENSMUSG00000024532.13"
## [309] "ENSMUSG00000040576.8" "ENSMUSG00000114630.1"
## [311] "ENSMUSG00000086467.2" "ENSMUSG00000031651.5"
## [313] "ENSMUSG00000099422.4" "ENSMUSG00000003153.10"
## [315] "ENSMUSG00000009549.14" "ENSMUSG00000073257.3"
## [317] "ENSMUSG00000095533.7" "ENSMUSG00000036992.10"
## [319] "ENSMUSG00000042200.3" "ENSMUSG00000096666.2"
## [321] "ENSMUSG00000047044.7" "ENSMUSG00000035165.14"
## [323] "ENSMUSG00000081604.5" "ENSMUSG00000010044.12"
## [325] "ENSMUSG00000063129.1" "ENSMUSG00000094843.2"
## [327] "ENSMUSG00000096153.1" "ENSMUSG00000028832.11"
## [329] "ENSMUSG00000028287.4" "ENSMUSG00000118504.1"
## [331] "ENSMUSG00000029182.10" "ENSMUSG00000037418.6"
## [333] "ENSMUSG00000012042.9" "ENSMUSG00000045886.7"
## [335] "ENSMUSG00000097075.3" "ENSMUSG00000045620.7"
## [337] "ENSMUSG00000023806.10" "ENSMUSG00000030654.9"
## [339] "ENSMUSG00000056486.18" "ENSMUSG00000109657.1"
## [341] "ENSMUSG00000057719.11" "ENSMUSG00000100727.6"
## [343] "ENSMUSG00000051728.7" "ENSMUSG00000086046.1"
## [345] "ENSMUSG00000040919.13" "ENSMUSG00000038165.8"
## [347] "ENSMUSG00000095546.7" "ENSMUSG00000081406.4"
## [349] "ENSMUSG00000015242.14" "ENSMUSG00000026743.16"
## [351] "ENSMUSG00000017049.4" "ENSMUSG00000059891.14"
## [353] "ENSMUSG00000015962.5" "ENSMUSG00000071726.2"
## [355] "ENSMUSG00000092522.1" "ENSMUSG00000090369.3"
## [357] "ENSMUSG00000026831.16" "ENSMUSG00000085580.1"
## [359] "ENSMUSG00000037894.13" "ENSMUSG00000026622.15"
## [361] "ENSMUSG00000030688.15" "ENSMUSG00000056987.8"
## [363] "ENSMUSG00000022641.15" "ENSMUSG00000027956.11"
## [365] "ENSMUSG00000061099.12" "ENSMUSG00000028716.15"
## [367] "ENSMUSG00000003923.14" "ENSMUSG00000030968.3"
## [369] "ENSMUSG00000022749.8" "ENSMUSG00000030301.17"
## [371] "ENSMUSG00000020048.13" "ENSMUSG00000028533.10"
## [373] "ENSMUSG00000045989.4" "ENSMUSG00000024223.3"
## [375] "ENSMUSG00000034689.2" "ENSMUSG00000028492.13"
## [377] "ENSMUSG00000107598.1" "ENSMUSG00000020681.14"
## [379] "ENSMUSG00000043429.7" "ENSMUSG00000072605.10"
## [381] "ENSMUSG00000001666.8" "ENSMUSG00000064363.1"
## [383] "ENSMUSG00000010841.13" "ENSMUSG00000051674.15"
## [385] "ENSMUSG00000044556.3" "ENSMUSG00000036533.9"
## [387] "ENSMUSG00000051896.4" "ENSMUSG00000118506.1"
## [389] "ENSMUSG00000095110.1" "ENSMUSG00000057173.8"
## [391] "ENSMUSG00000024510.6" "ENSMUSG00000079022.10"
## [393] "ENSMUSG00000029484.12" "ENSMUSG00000091849.7"
## [395] "ENSMUSG00000031971.15" "ENSMUSG00000030137.8"
## [397] "ENSMUSG00000102096.1" "ENSMUSG00000020696.18"
## [399] "ENSMUSG00000026107.11" "ENSMUSG00000032278.11"
## [401] "ENSMUSG00000019732.14" "ENSMUSG00000027793.6"
## [403] "ENSMUSG00000029044.9" "ENSMUSG00000001089.14"
## [405] "ENSMUSG00000029752.12" "ENSMUSG00000028520.12"
## [407] "ENSMUSG00000079409.8" "ENSMUSG00000028873.16"
## [409] "ENSMUSG00000094739.2" "ENSMUSG00000072145.3"
## [411] "ENSMUSG00000061104.5" "ENSMUSG00000078593.2"
## [413] "ENSMUSG00000045835.5" "ENSMUSG00000071103.10"
## [415] "ENSMUSG00000030747.5" "ENSMUSG00000026429.9"
## [417] "ENSMUSG00000025289.15" "ENSMUSG00000095606.7"
## [419] "ENSMUSG00000050471.17" "ENSMUSG00000050931.7"
## [421] "ENSMUSG00000028523.14" "ENSMUSG00000038085.13"
## [423] "ENSMUSG00000047654.6" "ENSMUSG00000073255.10"
## [425] "ENSMUSG00000069308.7" "ENSMUSG00000117725.1"
## [427] "ENSMUSG00000085785.7" "ENSMUSG00000087104.7"
## [429] "ENSMUSG00000042554.10" "ENSMUSG00000074734.3"
## [431] "ENSMUSG00000067338.6" "ENSMUSG00000024033.10"
## [433] "ENSMUSG00000095293.7" "ENSMUSG00000071721.5"
## [435] "ENSMUSG00000073247.3" "ENSMUSG00000073245.10"
## [437] "ENSMUSG00000071573.14" "ENSMUSG00000020640.10"
## [439] "ENSMUSG00000079184.10" "ENSMUSG00000024067.14"
## [441] "ENSMUSG00000028693.15" "ENSMUSG00000050612.6"
## [443] "ENSMUSG00000029320.11" "ENSMUSG00000099574.1"
## [445] "ENSMUSG00000059791.14" "ENSMUSG00000105185.4"
## [447] "ENSMUSG00000026466.16" "ENSMUSG00000030722.7"
## [449] "ENSMUSG00000033055.12" "ENSMUSG00000064370.1"
## [451] "ENSMUSG00000044405.4" "ENSMUSG00000084782.2"
## [453] "ENSMUSG00000032575.16" "ENSMUSG00000026239.14"
## [455] "ENSMUSG00000039742.15" "ENSMUSG00000064063.6"
## [457] "ENSMUSG00000074817.2" "ENSMUSG00000040097.16"
## [459] "ENSMUSG00000018776.10" "ENSMUSG00000054909.11"
## [461] "ENSMUSG00000029463.5" "ENSMUSG00000039183.6"
## [463] "ENSMUSG00000036770.11" "ENSMUSG00000034341.17"
## [465] "ENSMUSG00000031727.8" "ENSMUSG00000056665.2"
## [467] "ENSMUSG00000095887.7" "ENSMUSG00000020102.15"
## [469] "ENSMUSG00000094445.7" "ENSMUSG00000024209.9"
## [471] "ENSMUSG00000101113.1" "ENSMUSG00000079579.3"
## [473] "ENSMUSG00000054728.17" "ENSMUSG00000008822.15"
## [475] "ENSMUSG00000112657.1" "ENSMUSG00000044186.10"
## [477] "ENSMUSG00000047104.5" "ENSMUSG00000046826.7"
## [479] "ENSMUSG00000087279.10" "ENSMUSG00000029437.12"
## [481] "ENSMUSG00000064202.15" "ENSMUSG00000057805.4"
## [483] "ENSMUSG00000049506.7" "ENSMUSG00000046258.4"
## [485] "ENSMUSG00000024759.14" "ENSMUSG00000001473.7"
## [487] "ENSMUSG00000021687.14" "ENSMUSG00000093848.2"
## [489] "ENSMUSG00000032285.15" "ENSMUSG00000036964.14"
## [491] "ENSMUSG00000072726.3" "ENSMUSG00000042708.12"
## [493] "ENSMUSG00000090132.2" "ENSMUSG00000116376.1"
## [495] "ENSMUSG00000055177.15" "ENSMUSG00000054161.12"
## [497] "ENSMUSG00000022422.13" "ENSMUSG00000020401.6"
## [499] "ENSMUSG00000044084.2" "ENSMUSG00000095597.2"
## [501] "ENSMUSG00000051256.10" "ENSMUSG00000049008.4"
## [503] "ENSMUSG00000084995.8" "ENSMUSG00000095226.1"
## [505] "ENSMUSG00000085241.7" "ENSMUSG00000030275.6"
## [507] "ENSMUSG00000047733.10" "ENSMUSG00000038199.12"
## [509] "ENSMUSG00000016559.14" "ENSMUSG00000036168.15"
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## [1183] "ENSMUSG00000032204.13" "ENSMUSG00000100240.1"
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## [1187] "ENSMUSG00000094258.7" "ENSMUSG00000020633.14"
## [1189] "ENSMUSG00000031458.8" "ENSMUSG00000089982.7"
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## [1193] "ENSMUSG00000028451.12" "ENSMUSG00000085486.2"
## [1195] "ENSMUSG00000026523.14" "ENSMUSG00000004341.8"
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## [1199] "ENSMUSG00000002949.15" "ENSMUSG00000112141.1"
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## [1203] "ENSMUSG00000101915.1" "ENSMUSG00000028383.17"
## [1205] "ENSMUSG00000083287.4" "ENSMUSG00000025903.14"
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## [1213] "ENSMUSG00000002957.11" "ENSMUSG00000056815.1"
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## [1221] "ENSMUSG00000103935.1" "ENSMUSG00000082398.1"
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## [1235] "ENSMUSG00000063145.10" "ENSMUSG00000031270.1"
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## [1241] "ENSMUSG00000076436.1" "ENSMUSG00000073821.11"
## [1243] "ENSMUSG00000086587.7" "ENSMUSG00000031818.12"
## [1245] "ENSMUSG00000056260.15" "ENSMUSG00000027099.9"
## [1247] "ENSMUSG00000032399.8" "ENSMUSG00000074247.10"
## [1249] "ENSMUSG00000070369.13" "ENSMUSG00000091243.2"
## [1251] "ENSMUSG00000046282.7" "ENSMUSG00000027364.14"
## [1253] "ENSMUSG00000034601.17" "ENSMUSG00000021143.10"
## [1255] "ENSMUSG00000007739.10" "ENSMUSG00000034248.7"
## [1257] "ENSMUSG00000024959.14" "ENSMUSG00000021986.9"
## [1259] "ENSMUSG00000038515.10" "ENSMUSG00000026778.13"
## [1261] "ENSMUSG00000020283.5" "ENSMUSG00000024500.20"
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## [1269] "ENSMUSG00000034245.10" "ENSMUSG00000118332.1"
## [1271] "ENSMUSG00000047368.4" "ENSMUSG00000050435.2"
## [1273] "ENSMUSG00000030978.10" "ENSMUSG00000018362.14"
## [1275] "ENSMUSG00000008855.17" "ENSMUSG00000026729.9"
## [1277] "ENSMUSG00000028789.16" "ENSMUSG00000096016.7"
## [1279] "ENSMUSG00000117104.1" "ENSMUSG00000109228.2"
## [1281] "ENSMUSG00000069118.3" "ENSMUSG00000037236.16"
## [1283] "ENSMUSG00000090307.7" "ENSMUSG00000085197.7"
## [1285] "ENSMUSG00000032238.17" "ENSMUSG00000051329.13"
## [1287] "ENSMUSG00000032177.17" "ENSMUSG00000028389.12"
## [1289] "ENSMUSG00000044795.12" "ENSMUSG00000024317.15"
## [1291] "ENSMUSG00000002210.11" "ENSMUSG00000029103.16"
## [1293] "ENSMUSG00000115656.1" "ENSMUSG00000032475.15"
## [1295] "ENSMUSG00000035293.13" "ENSMUSG00000100336.1"
## [1297] "ENSMUSG00000036427.5" "ENSMUSG00000092586.8"
## [1299] "ENSMUSG00000026499.5" "ENSMUSG00000022884.15"
## [1301] "ENSMUSG00000091792.1" "ENSMUSG00000100559.1"
## [1303] "ENSMUSG00000057047.5" "ENSMUSG00000021977.11"
## [1305] "ENSMUSG00000094845.2" "ENSMUSG00000039179.13"
## [1307] "ENSMUSG00000085660.1" "ENSMUSG00000068391.8"
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## [1313] "ENSMUSG00000060161.9" "ENSMUSG00000032221.14"
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## [1317] "ENSMUSG00000006310.10" "ENSMUSG00000035142.18"
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## [1323] "ENSMUSG00000093923.7" "ENSMUSG00000080268.4"
## [1325] "ENSMUSG00000061928.6" "ENSMUSG00000008813.13"
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## [1329] "ENSMUSG00000022538.20" "ENSMUSG00000117310.2"
## [1331] "ENSMUSG00000047215.14" "ENSMUSG00000066278.6"
## [1333] "ENSMUSG00000028563.16" "ENSMUSG00000046949.16"
## [1335] "ENSMUSG00000111078.1" "ENSMUSG00000072919.4"
## [1337] "ENSMUSG00000041355.13" "ENSMUSG00000038150.7"
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## [1341] "ENSMUSG00000099894.1" "ENSMUSG00000058022.14"
## [1343] "ENSMUSG00000115372.1" "ENSMUSG00000048100.13"
## [1345] "ENSMUSG00000040659.3" "ENSMUSG00000064307.13"
## [1347] "ENSMUSG00000115896.1" "ENSMUSG00000117497.1"
## [1349] "ENSMUSG00000052738.14" "ENSMUSG00000052403.11"
## [1351] "ENSMUSG00000113179.1" "ENSMUSG00000046367.10"
## [1353] "ENSMUSG00000039841.14" "ENSMUSG00000095296.7"
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## [1357] "ENSMUSG00000024076.10" "ENSMUSG00000021101.2"
## [1359] "ENSMUSG00000109293.1" "ENSMUSG00000025257.5"
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## [1363] "ENSMUSG00000021620.4" "ENSMUSG00000028657.14"
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## [1493] "ENSMUSG00000047046.8" "ENSMUSG00000097717.2"
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## [1967] "ENSMUSG00000042688.16" "ENSMUSG00000040822.7"
## [1969] "ENSMUSG00000095452.2" "ENSMUSG00000090379.1"
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## [1989] "ENSMUSG00000022111.9" "ENSMUSG00000030264.14"
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## [1993] "ENSMUSG00000020463.15" "ENSMUSG00000029707.6"
## [1995] "ENSMUSG00000111028.1" "ENSMUSG00000019878.8"
## [1997] "ENSMUSG00000022965.8" "ENSMUSG00000085759.1"
## [1999] "ENSMUSG00000087185.1" "ENSMUSG00000086732.1"
##
## $timestamp
## [1] "2026-07-05 20:46:46 UTC"9.2.3 Visualize velocity-based trajectory
Once the velocity state is recorded, visualizing it is a breeze. You can use VelocityPlot() to draw the dynamic stream or arrows over any active dimensionality reduction space (like UMAP or t-SNE).
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Installing pyenv ...
## Done! pyenv has been installed to '/home/runner/.local/share/r-reticulate/pyenv/bin/pyenv'.
## Using Python: /home/runner/.pyenv/versions/3.12.10/bin/python3.12
## Creating virtual environment '/home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env' ...## + /home/runner/.pyenv/versions/3.12.10/bin/python3.12 -m venv /home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env## Done!
## Installing packages: pip, wheel, setuptools## + /home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env/bin/python -m pip install --upgrade pip wheel setuptools## Installing packages: 'anndata==0.11.4', 'array-api-compat==1.12.0', 'click==8.2.1', 'contourpy==1.3.2', 'cycler==0.12.1', 'fonttools==4.58.5', 'h5py==3.14.0', 'joblib==1.5.1', 'kiwisolver==1.4.8', 'legacy-api-wrap==1.4.1', 'llvmlite==0.44.0', 'loompy==3.0.8', 'matplotlib==3.10.3', 'natsort==8.4.0', 'networkx==3.5', 'numba==0.61.2', 'numpy==2.2.6', 'numpy-groupies==0.11.3', 'packaging==25.0', 'pandas==2.3.1', 'patsy==1.0.1', 'pillow==11.3.0', 'pip==25.1.1', 'pynndescent==0.5.13', 'pyparsing==3.2.3', 'python-dateutil==2.9.0.post0', 'pytz==2025.2', 'scanpy==1.11.3', 'scikit-learn==1.7.0', 'scipy==1.15.3', 'scvelo==0.3.3', 'seaborn==0.13.2', 'session-info2==0.1.2', 'setuptools==80.9.0', 'six==1.17.0', 'statsmodels==0.14.5', 'threadpoolctl==3.6.0', 'tqdm==4.67.1', 'typing_extensions==4.14.1', 'tzdata==2025.2', 'umap-learn==0.5.9.post2', 'wheel==0.45.1'## + /home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env/bin/python -m pip install --upgrade --no-user 'anndata==0.11.4' 'array-api-compat==1.12.0' 'click==8.2.1' 'contourpy==1.3.2' 'cycler==0.12.1' 'fonttools==4.58.5' 'h5py==3.14.0' 'joblib==1.5.1' 'kiwisolver==1.4.8' 'legacy-api-wrap==1.4.1' 'llvmlite==0.44.0' 'loompy==3.0.8' 'matplotlib==3.10.3' 'natsort==8.4.0' 'networkx==3.5' 'numba==0.61.2' 'numpy==2.2.6' 'numpy-groupies==0.11.3' 'packaging==25.0' 'pandas==2.3.1' 'patsy==1.0.1' 'pillow==11.3.0' 'pip==25.1.1' 'pynndescent==0.5.13' 'pyparsing==3.2.3' 'python-dateutil==2.9.0.post0' 'pytz==2025.2' 'scanpy==1.11.3' 'scikit-learn==1.7.0' 'scipy==1.15.3' 'scvelo==0.3.3' 'seaborn==0.13.2' 'session-info2==0.1.2' 'setuptools==80.9.0' 'six==1.17.0' 'statsmodels==0.14.5' 'threadpoolctl==3.6.0' 'tqdm==4.67.1' 'typing_extensions==4.14.1' 'tzdata==2025.2' 'umap-learn==0.5.9.post2' 'wheel==0.45.1'## Virtual environment '/home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env' successfully created.## For native R and reading and writing of H5AD files, an R
## <AnnData> object, and conversion to <SingleCellExperiment>
## or <Seurat> objects, check out the anndataR package:
## ℹ Install it from Bioconductor with
## `BiocManager::install("anndataR")`
## ℹ See more at <https://bioconductor.org/packages/anndataR/>
## This message is displayed once per session.## ℹ Using the 'X' assay as the X matrix## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## computing velocity embedding
## finished (0:00:00) --> added
## 'velocity_target', embedded velocity vectors (adata.obsm)
9.3 CellRank: Advanced Fate Mapping
When standard trajectory tools (like Slingshot) struggle with complex, cyclic, or highly heterogeneous developmental processes, CellRank shines. CellRank elegantly combines directed RNA velocity data with undirected transcriptomic similarity to robustly infer terminal states and cellular fate probabilities.
sclet brings the full power of CellRank directly to your SCE object, again utilizing the isolated basilisk Python environment to prevent dependency conflicts.
9.3.1 Run CellRank
RunCellFate() is the user-facing entry point for fate mapping in sclet. At the moment it dispatches to CellRank, automatically senses the upstream velocity run, and records the resulting terminal states, named fate probabilities, and lineage drivers in the shared state contract.
## $id
## [1] "cellrank"
##
## $type
## [1] "trajectory"
##
## $status
## [1] "completed"
##
## $method
## [1] "CellRank"
##
## $inputs
## $inputs$reduction
## [1] "PCA"
##
## $inputs$cluster_key
## [1] "cluster"
##
## $inputs$velocity_id
## [1] "velocity"
##
##
## $artifacts
## $artifacts$analysis_key
## [1] "cellrank"
##
## $artifacts$terminal_state_col
## [1] "cellrank_terminal_states"
##
## $artifacts$fate_probability_cols
## [1] "cellrank_fate_X0" "cellrank_fate_X1"
##
## $artifacts$fate_probability_names
## [1] "0" "1"
##
## $artifacts$has_lineage_drivers
## [1] TRUE
##
##
## $params
## list()
##
## $summary
## $summary$n_terminal_states
## [1] 2
##
## $summary$n_fate_dimensions
## [1] 2
##
## $summary$n_lineage_drivers
## [1] 4000
##
##
## $reduction
## [1] "PCA"
##
## $cluster_key
## [1] "cluster"
##
## $terminal_states
## [1] NA NA NA "0" NA NA "1" NA NA NA NA NA NA
## [14] NA "0" NA NA NA NA NA "1" NA NA NA NA "1"
## [27] NA "0" "1" NA "0" NA "0" NA "0" NA NA "0" NA
## [40] NA "0" NA NA NA NA "0" NA NA NA "0" NA NA
## [53] NA "0" NA NA NA NA NA NA NA NA NA "1" NA
## [66] NA "0" NA NA NA NA NA NA NA "1" NA "0" NA
## [79] NA NA NA NA "1" NA "0" "1" "0" NA NA "0" NA
## [92] "0" NA "0" NA NA NA NA NA NA NA "0" NA NA
## [105] "1" NA NA "1" NA NA NA "1" NA NA NA "1" NA
## [118] "1" NA NA NA "1" NA "0" "0" NA NA NA NA NA
## [131] NA NA "1" NA "1" NA NA NA NA NA NA NA NA
## [144] "1" NA NA NA NA NA "1" NA NA "1" NA NA "1"
## [157] NA NA NA NA NA "1" "0" NA NA "1" NA NA NA
## [170] NA NA "0" NA NA NA NA NA "1" NA NA NA NA
## [183] NA NA NA NA "0" NA NA NA NA NA NA NA "1"
## [196] NA NA NA NA NA "1" NA NA NA NA NA "0" "0"
## [209] "1" NA NA NA "0" NA NA NA NA NA NA NA NA
## [222] NA NA NA NA NA NA NA NA NA NA NA NA NA
## [235] NA "1" NA NA NA NA NA NA NA NA NA NA NA
## [248] NA NA NA NA NA NA NA NA NA NA NA NA NA
## [261] NA NA NA NA NA NA NA NA NA NA NA "1" NA
## [274] NA NA "1" NA NA NA NA NA NA NA NA NA "0"
## [287] NA NA "1" NA NA NA "0" NA NA NA NA "0" NA
## [300] NA
##
## $absorption_probs
## cellrank_fate_X0 cellrank_fate_X1
## [1,] 0.99702079 0.002979403
## [2,] 0.99554624 0.004453895
## [3,] 0.99467236 0.005327871
## [4,] 1.00000000 0.000000000
## [5,] 0.93386362 0.066128651
## [6,] 0.93386457 0.066127800
## [7,] 0.00000000 1.000000000
## [8,] 0.93386484 0.066127578
## [9,] 0.93386475 0.066127619
## [10,] 0.99821091 0.001789189
## [11,] 0.93387051 0.066121807
## [12,] 0.93386347 0.066128800
## [13,] 0.93386447 0.066127933
## [14,] 0.93386322 0.066129000
## [15,] 1.00000000 0.000000000
## [16,] 0.99687145 0.003128671
## [17,] 0.93386289 0.066129439
## [18,] 0.93386504 0.066127104
## [19,] 0.93386285 0.066129504
## [20,] 0.97175552 0.028242821
## [21,] 0.00000000 1.000000000
## [22,] 0.93386475 0.066127553
## [23,] 0.93385668 0.066135557
## [24,] 0.93386069 0.066131591
## [25,] 0.93385716 0.066135183
## [26,] 0.00000000 1.000000000
## [27,] 0.93386478 0.066127350
## [28,] 1.00000000 0.000000000
## [29,] 0.00000000 1.000000000
## [30,] 0.93390299 0.066089163
## [31,] 1.00000000 0.000000000
## [32,] 0.93334962 0.066642696
## [33,] 1.00000000 0.000000000
## [34,] 0.93386041 0.066131935
## [35,] 1.00000000 0.000000000
## [36,] 0.93384886 0.066143499
## [37,] 0.93387567 0.066116468
## [38,] 1.00000000 0.000000000
## [39,] 0.93386501 0.066127389
## [40,] 0.93386190 0.066130472
## [41,] 1.00000000 0.000000000
## [42,] 0.93386967 0.066122668
## [43,] 0.93386332 0.066128985
## [44,] 0.93386477 0.066127432
## [45,] 0.93386470 0.066127596
## [46,] 1.00000000 0.000000000
## [47,] 0.93386426 0.066128167
## [48,] 0.92909910 0.070893316
## [49,] 0.93386470 0.066127504
## [50,] 1.00000000 0.000000000
## [51,] 0.99265539 0.007344720
## [52,] 0.93386473 0.066127449
## [53,] 0.93386485 0.066127382
## [54,] 1.00000000 0.000000000
## [55,] 0.93386459 0.066127637
## [56,] 0.93386497 0.066127416
## [57,] 0.93386104 0.066131268
## [58,] 0.99432502 0.005675160
## [59,] 0.98319042 0.016809800
## [60,] 0.93386624 0.066125988
## [61,] 0.93382855 0.066163772
## [62,] 0.93381615 0.066176161
## [63,] 0.93386400 0.066128318
## [64,] 0.00000000 1.000000000
## [65,] 0.93386327 0.066129077
## [66,] 0.12193963 0.878060505
## [67,] 1.00000000 0.000000000
## [68,] 0.93386515 0.066127189
## [69,] 0.97653877 0.023461592
## [70,] 0.93390455 0.066087669
## [71,] 0.89391967 0.106080512
## [72,] 0.93386482 0.066127613
## [73,] 0.93386417 0.066128020
## [74,] 0.93386473 0.066127690
## [75,] 0.00000000 1.000000000
## [76,] 0.93385851 0.066133787
## [77,] 1.00000000 0.000000000
## [78,] 0.93386474 0.066127388
## [79,] 0.99423855 0.005761593
## [80,] 0.93386219 0.066130014
## [81,] 0.93386440 0.066127872
## [82,] 0.93389593 0.066096448
## [83,] 0.00000000 1.000000000
## [84,] 0.93386491 0.066127466
## [85,] 1.00000000 0.000000000
## [86,] 0.00000000 1.000000000
## [87,] 1.00000000 0.000000000
## [88,] 0.62144752 0.378553150
## [89,] 0.93386492 0.066127349
## [90,] 1.00000000 0.000000000
## [91,] 0.93386485 0.066127480
## [92,] 1.00000000 0.000000000
## [93,] 0.93386415 0.066128151
## [94,] 1.00000000 0.000000000
## [95,] 0.93386451 0.066127718
## [96,] 0.93386425 0.066128103
## [97,] 0.93386145 0.066130878
## [98,] 0.93386377 0.066128505
## [99,] 0.93386314 0.066129165
## [100,] 0.93385296 0.066139439
## [101,] 0.93386964 0.066122581
## [102,] 1.00000000 0.000000000
## [103,] 0.93386467 0.066127536
## [104,] 0.93387900 0.066112932
## [105,] 0.00000000 1.000000000
## [106,] 0.93386574 0.066126516
## [107,] 0.76093938 0.239061206
## [108,] 0.00000000 1.000000000
## [109,] 0.99692364 0.003076577
## [110,] 0.99418059 0.005819583
## [111,] 0.93386499 0.066127398
## [112,] 0.00000000 1.000000000
## [113,] 0.93386441 0.066127765
## [114,] 0.93386062 0.066131732
## [115,] 0.93386472 0.066127466
## [116,] 0.00000000 1.000000000
## [117,] 0.62985065 0.370149977
## [118,] 0.00000000 1.000000000
## [119,] 0.93387443 0.066117638
## [120,] 0.99355631 0.006443791
## [121,] 0.93386112 0.066131163
## [122,] 0.00000000 1.000000000
## [123,] 0.93386467 0.066127510
## [124,] 1.00000000 0.000000000
## [125,] 1.00000000 0.000000000
## [126,] 0.93387900 0.066112932
## [127,] 0.93386471 0.066127502
## [128,] 0.92666452 0.073327867
## [129,] 0.93386477 0.066127395
## [130,] 0.08816117 0.911838925
## [131,] 0.93386452 0.066127757
## [132,] 0.93386451 0.066127732
## [133,] 0.00000000 1.000000000
## [134,] 0.66998783 0.330012701
## [135,] 0.00000000 1.000000000
## [136,] 0.92329507 0.076705143
## [137,] 0.93386401 0.066128299
## [138,] 0.93386549 0.066126907
## [139,] 0.93385910 0.066133087
## [140,] 0.93385648 0.066135847
## [141,] 0.93383087 0.066161453
## [142,] 0.78929234 0.210708332
## [143,] 0.93385465 0.066137592
## [144,] 0.00000000 1.000000000
## [145,] 0.93386058 0.066131662
## [146,] 0.99388134 0.006118856
## [147,] 0.32868802 0.671312246
## [148,] 0.93387187 0.066120268
## [149,] 0.93386101 0.066131304
## [150,] 0.00000000 1.000000000
## [151,] 0.93402744 0.065965193
## [152,] 0.82595531 0.174044967
## [153,] 0.00000000 1.000000000
## [154,] 0.93386430 0.066127947
## [155,] 0.99560129 0.004399008
## [156,] 0.00000000 1.000000000
## [157,] 0.93076723 0.069225101
## [158,] 0.93385871 0.066133570
## [159,] 0.93385845 0.066133796
## [160,] 0.93384925 0.066143148
## [161,] 0.83934038 0.160660113
## [162,] 0.00000000 1.000000000
## [163,] 1.00000000 0.000000000
## [164,] 0.93388986 0.066102114
## [165,] 0.93390455 0.066087669
## [166,] 0.00000000 1.000000000
## [167,] 0.93386466 0.066127466
## [168,] 0.93386202 0.066130302
## [169,] 0.93386097 0.066131330
## [170,] 0.93386463 0.066127532
## [171,] 0.93389418 0.066097984
## [172,] 1.00000000 0.000000000
## [173,] 0.93386388 0.066128410
## [174,] 0.93386482 0.066127526
## [175,] 0.93387697 0.066115044
## [176,] 0.97710740 0.022892836
## [177,] 0.93386463 0.066127732
## [178,] 0.00000000 1.000000000
## [179,] 0.93379778 0.066194510
## [180,] 0.93388457 0.066107405
## [181,] 0.93386488 0.066127517
## [182,] 0.93387586 0.066116270
## [183,] 0.98860737 0.011392952
## [184,] 0.93388617 0.066105799
## [185,] 0.93386369 0.066128570
## [186,] 0.93386480 0.066127342
## [187,] 1.00000000 0.000000000
## [188,] 0.99491412 0.005086141
## [189,] 0.93386521 0.066127201
## [190,] 0.93386861 0.066123469
## [191,] 0.93386491 0.066127320
## [192,] 0.93324070 0.066751603
## [193,] 0.93346054 0.066531775
## [194,] 0.93386631 0.066125851
## [195,] 0.00000000 1.000000000
## [196,] 0.93386826 0.066123973
## [197,] 0.93314359 0.066848698
## [198,] 0.93385959 0.066132667
## [199,] 0.93382122 0.066171084
## [200,] 0.93380224 0.066189999
## [201,] 0.00000000 1.000000000
## [202,] 0.93336645 0.066625819
## [203,] 0.93387447 0.066117714
## [204,] 0.93387034 0.066121963
## [205,] 0.93390455 0.066087669
## [206,] 0.93386436 0.066128009
## [207,] 1.00000000 0.000000000
## [208,] 1.00000000 0.000000000
## [209,] 0.00000000 1.000000000
## [210,] 0.93390063 0.066091497
## [211,] 0.93387379 0.066118474
## [212,] 0.93386486 0.066127430
## [213,] 1.00000000 0.000000000
## [214,] 0.93386348 0.066128881
## [215,] 0.93386792 0.066124133
## [216,] 0.93390455 0.066087669
## [217,] 0.97959613 0.020404196
## [218,] 0.93386457 0.066127872
## [219,] 0.93386389 0.066128432
## [220,] 0.43064670 0.569353785
## [221,] 0.93386260 0.066129732
## [222,] 0.93386454 0.066127741
## [223,] 0.93386480 0.066127294
## [224,] 0.93386456 0.066127878
## [225,] 0.93384971 0.066142662
## [226,] 0.93390455 0.066087669
## [227,] 0.93386378 0.066128468
## [228,] 0.93386468 0.066127649
## [229,] 0.93390455 0.066087669
## [230,] 0.93385860 0.066133708
## [231,] 0.93386475 0.066127389
## [232,] 0.93386476 0.066127395
## [233,] 0.93386542 0.066126994
## [234,] 0.93386694 0.066125346
## [235,] 0.93386174 0.066130530
## [236,] 0.00000000 1.000000000
## [237,] 0.93386486 0.066127334
## [238,] 0.93386963 0.066122531
## [239,] 0.93386388 0.066128496
## [240,] 0.93390666 0.066085586
## [241,] 0.93386798 0.066124090
## [242,] 0.93387223 0.066119877
## [243,] 0.93386587 0.066126336
## [244,] 0.93386568 0.066126724
## [245,] 0.93386091 0.066131338
## [246,] 0.93385774 0.066134686
## [247,] 0.93386518 0.066127233
## [248,] 0.93387518 0.066117064
## [249,] 0.93386574 0.066126619
## [250,] 0.93386420 0.066128089
## [251,] 0.93389725 0.066094850
## [252,] 0.93389941 0.066092710
## [253,] 0.93386033 0.066132036
## [254,] 0.93386460 0.066127767
## [255,] 0.93386477 0.066127364
## [256,] 0.93386482 0.066127579
## [257,] 0.93386757 0.066124483
## [258,] 0.93386453 0.066127648
## [259,] 0.93386472 0.066127488
## [260,] 0.99576620 0.004234121
## [261,] 0.93384366 0.066148669
## [262,] 0.93386614 0.066126079
## [263,] 0.93386263 0.066129711
## [264,] 0.93386094 0.066131360
## [265,] 0.95671778 0.043282381
## [266,] 0.93213050 0.067861904
## [267,] 0.93390455 0.066087669
## [268,] 0.93386442 0.066127835
## [269,] 0.93329078 0.066701493
## [270,] 0.93386193 0.066130405
## [271,] 0.93386488 0.066127555
## [272,] 0.00000000 1.000000000
## [273,] 0.93386458 0.066127765
## [274,] 0.93386478 0.066127339
## [275,] 0.93386791 0.066124141
## [276,] 0.00000000 1.000000000
## [277,] 0.93386432 0.066127959
## [278,] 0.93387005 0.066122216
## [279,] 0.93389706 0.066095000
## [280,] 0.93386468 0.066127554
## [281,] 0.93386663 0.066125559
## [282,] 0.93386333 0.066128969
## [283,] 0.93386516 0.066127066
## [284,] 0.93386429 0.066127986
## [285,] 0.07872847 0.921271639
## [286,] 1.00000000 0.000000000
## [287,] 0.93385327 0.066139061
## [288,] 0.93386467 0.066127714
## [289,] 0.00000000 1.000000000
## [290,] 0.93386795 0.066124025
## [291,] 0.93386482 0.066127309
## [292,] 0.93392455 0.066067751
## [293,] 1.00000000 0.000000000
## [294,] 0.93386686 0.066125288
## [295,] 0.93386481 0.066127662
## [296,] 0.93386522 0.066127216
## [297,] 0.93376035 0.066231961
## [298,] 1.00000000 0.000000000
## [299,] 0.90631186 0.093680681
## [300,] 0.99499636 0.005003830
##
## $terminal_state_col
## [1] "cellrank_terminal_states"
##
## $fate_probability_cols
## [1] "cellrank_fate_X0" "cellrank_fate_X1"
##
## $fate_probability_names
## [1] "0" "1"
##
## $lineage_drivers
## # A tibble: 4,000 × 7
## gene lineage corr pval qval ci_low ci_high
## <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 ENSMUS… 0 -0.147 1.10e- 2 1.54e-2 -0.256 -0.0339
## 2 ENSMUS… 0 -0.00858 8.82e- 1 8.91e-1 -0.122 0.105
## 3 ENSMUS… 0 0.344 6.75e-10 5.47e-9 0.240 0.440
## 4 ENSMUS… 0 -0.306 5.17e- 8 2.21e-7 -0.405 -0.200
## 5 ENSMUS… 0 -0.203 3.86e- 4 7.02e-4 -0.309 -0.0920
## 6 ENSMUS… 0 0.248 1.30e- 5 3.06e-5 0.138 0.351
## 7 ENSMUS… 0 0.0138 8.12e- 1 8.24e-1 -0.0996 0.127
## 8 ENSMUS… 0 -0.341 9.82e-10 7.70e-9 -0.437 -0.236
## 9 ENSMUS… 0 -0.141 1.47e- 2 2.01e-2 -0.250 -0.0278
## 10 ENSMUS… 0 0.320 1.09e- 8 5.87e-8 0.215 0.418
## # ℹ 3,990 more rows
##
## $created_at
## [1] "2026-07-05 21:01:26 UTC"
##
## $timestamp
## [1] "2026-07-05 21:01:26 UTC"The resulting terminal state assignments and directional fate probabilities are written directly into colData(sce). In addition, sclet now provides fate-specific plotting helpers following the plot_<module>_<type> convention, so you do not need to manually reconstruct the plotting data frame after every run.
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'
cr <- get_cellrank(sce, id = "cellrank")
driver_lineage <- if (!is.null(cr$artifacts$fate_probability_names)) {
cr$artifacts$fate_probability_names[[1]]
} else {
cr$fate_probability_names[[1]]
}
plot_fate_driver_trends(sce, lineage = driver_lineage, top_n = 4)
9.4 Already have RegVelo results? Wiring them into CellRank
RegVelo extends RNA velocity inference by using a prior gene regulatory network, and in practice it is most useful when run on a GPU-enabled Python environment. If that is your situation, this section answers the immediate follow-up question: the GPU step produced a velocity result — how does it get consumed by CellRank without leaving the sclet state layer? The book build does not provision GPU resources, so this section follows the same cache-first pattern as the heavier CellRank examples above: the GPU step is shown as runnable user code, but the rendered book reads a precomputed SingleCellExperiment from bookdown/data.
The upstream run uses spliced and unspliced assays plus a prior GRN, writes the inferred velocity matrix back into the object as a named assay, and then hands that stored velocity result to CellRank. This code is intentionally not executed during book rendering.
# Run this on a GPU server, not during book rendering.
sce <- RunRegVelo(
sce,
grn = prior_grn,
reduction = "PCA",
name = "regvelo_smoke",
backend = "reticulate",
python = "/path/to/gpu/venv/bin/python",
max_epochs = 20,
batch_size = 128
)
sce <- RunCellRank(
sce,
reduction = "PCA",
cluster_key = "celltype_or_cluster",
velocity_id = "regvelo_smoke",
backend = "reticulate",
python = "/path/to/gpu/venv/bin/python",
name = "cellrank_regvelo_smoke"
)
saveRDS(sce, "bookdown/data/regvelo-smoke-cellrank.rds")The cached object below was generated outside the book render. It lets the documentation demonstrate downstream inspection and plotting without rerunning PyTorch, RegVelo, or CellRank on the GitHub Actions worker.
regvelo_sce <- readRDS("data/regvelo-smoke-cellrank.rds")
get_velocity(regvelo_sce, id = "regvelo_smoke")$artifacts## $velocity_assay
## [1] "regvelo_smoke_velocity"
##
## $colData
## character(0)
##
## $rowData
## character(0)
##
## $analysis_key
## [1] "regvelo_smoke"## metric value
## 1 n_cells 300
## 2 n_terminal_states 1
## 3 n_fate_dimensions 1
## 4 has_lineage_drivers FALSE
## 5 terminal_state_col cellrank_terminal_states
## 6 fate_probability_cols cellrank_fate_X0## terminal_state n_cells
## 1 0 30
## 2 Unassigned 270## fate_probability_col min median max
## 1 cellrank_fate_X0 0.9999995 1 1.000001
## sd
## 1 2.458258e-07## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'p_genes <- plot_top_velocity_genes(regvelo_sce, id = "regvelo_smoke", n = 15)
plot_list(`Velocity Magnitude` = p_mag, `Top Velocity Genes` = p_genes)
p_regvelo_term <- plot_fate_terminal_states(
regvelo_sce,
id = "cellrank_regvelo_smoke",
reduction = "PCA"
)## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'p_regvelo_fate <- plot_fate_probability(
regvelo_sce,
id = "cellrank_regvelo_smoke",
fate = 1,
reduction = "PCA"
)## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'## Also defined by 'alabaster.base'
VelocityFateCorrelation(
regvelo_sce,
velocity_id = "regvelo_smoke",
trajectory_id = "cellrank_regvelo_smoke"
)## fate_probability_col velocity_assay method
## 1 cellrank_fate_X0 regvelo_smoke_velocity spearman
## n_cells estimate p_value
## 1 300 0.3538271 2.824656e-10plot_velocity_fate_correlation(
regvelo_sce,
velocity_id = "regvelo_smoke",
trajectory_id = "cellrank_regvelo_smoke"
)
In this small smoke-test object, CellRank detects only one terminal state and the single fate probability is effectively constant. That is still useful as a workflow check: it confirms that the RegVelo velocity assay can be consumed by the CellRank wrapper and downstream visualization. For biological interpretation, a real dataset should usually show multiple terminal states or nontrivial fate probability gradients.
9.5 Workflow shell for velocity and fate
This closes the loop on question 1: when spliced/unspliced assays are available, the same trajectory mainline can extend from lineage inference to velocity and fate mapping in a single call — every stage still lands in the state layer under one workflow record:
sce <- RunTrajectoryWorkflow(
sce,
group = "cluster",
reduction = "PCA",
run_diffusion_map = FALSE,
run_slingshot = FALSE,
run_velocity = "auto",
run_fate = "auto",
name = "germline_main"
)
plot_trajectory_overview(
sce,
id = "germline_main",
panels = c("velocity", "terminal_states", "fate_probability")
)9.6 Is it real or a smoke screen? Diagnosing the velocity-fate chain
This is question 3, and answering it well is what makes the other two questions worth asking. A velocity-fate chain can execute cleanly from end to end and still be biologically empty: a degenerate velocity field will happily produce one dominant terminal state backed by an essentially constant fate probability. The trick is that none of this requires rerunning Python — because RunCellRank() and RunVelocity() write their results into the state layer, every diagnostic below reads cached records directly.
The helpers shown here (CellRankSummary(), VelocityFateCorrelation(), plot_velocity_magnitude(), plot_top_velocity_genes()) were all demonstrated on the RegVelo cache above; this section explains how to read them.
9.6.1 Reading the CellRank summary
Three things in the CellRankSummary() output deserve attention before you interpret anything else:
- Number of terminal states. One terminal state on a development-style dataset usually means the transition matrix collapsed — either the velocity field is too weak, or the neighborhood graph is dominated by one cluster. Treat it as a workflow smoke check, not biology.
- Size balance of terminal states (
terminal_statestable). A “terminal” state holding a handful of cells is more likely an artifact of the kNN graph than a genuine sink. - Shape of the fate probabilities (
fate_probabilitiestable). Compare min/median/max per fate column: if max - median is near zero, fate probability carries no cell-to-cell information and downstream gene drivers inherit that flatness.
That is exactly the situation in the smoke-test object above: single terminal state, effectively constant fate probability. Useful as proof that the RegVelo assay was consumed correctly; useless as a developmental claim. A publishable result needs multiple terminal states or a nontrivial fate gradient.
9.6.2 Does velocity actually explain fate?
VelocityFateCorrelation() pairs per-cell velocity magnitude against fate probability, and plot_velocity_fate_correlation() renders the scatter. How to read it:
- Positive correlation: cells moving fast also have committed fates — consistent with the velocity field actively driving absorption.
- Near-zero correlation: fate probabilities exist but appear decoupled from velocity. Common causes include over-smoothed the diffusion kernel, a prior GRN (RegVelo) that regularized away most of the signal, or simply few genes with informative unspliced counts.
- Inversion (strongly negative): rare, but usually points at sign errors or a mismatch between the reduction used for velocity projection and the one used for fate computation.
Also glance at plot_velocity_magnitude() and plot_top_velocity_genes(): if the top-gene list is full of low-count noise instead of biology you recognize, the kinetic estimate itself is the weak link — fix that before tuning CellRank parameters.
9.6.3 Auditing the whole chain in one place
Because each stage logs a command record, the full provenance of a (possibly suspicious) result is inspectable without recomputation:
## command timestamp
## 1 RunRegVelo 2026-07-01 07:21:23
## 2 RunCellRank 2026-07-02 01:11:07
## params_summary
## 1 spliced_assay=spliced; unspliced_assay=unspliced; reduction=PCA; name=regvelo_smoke; max_epochs=20; lam=1; lam2=0; batch_size=128; seed=1; backend=reticulate; python=/biostack/home/guangchuang/sclet/.venv-regvelo/bin/python
## 2 reduction=PCA; cluster_key=regvelo_smoke_cluster; velocity_id=regvelo_smoke; backend=reticulate; python=/biostack/home/guangchuang/sclet/.venv-regvelo/bin/python; name=cellrank_regvelo_smoke
## outputs_summary
## 1 analysis=velocity; velocity=regvelo_smoke; assay=regvelo_smoke_velocity
## 2 analysis=cellrank; trajectory=cellrank_regvelo_smoke## velocity trajectory
## TRUE TRUEIf a figure looks wrong, read the command log backwards: which id produced it, with which parameters, fed by which upstream state. Nine times out of ten the problem is visible there before you touch any plot.
9.7 Velocity Latent Time
When scVelo is run in dynamical mode, it infers a latent time for each cell — a pseudotime ordering derived from the RNA velocity field itself, not from a separate trajectory method. plot_velocity_latent_time() colors cells on an embedding by this inferred temporal progression.
References
Bergen, Volker, Marius Lange, Stefan Peidli, F. Alexander Wolf, and Fabian J. Theis. 2020. “Generalizing RNA Velocity to Transient Cell States Through Dynamical Modeling.” Nature Biotechnology 38 (12): 1408–14. https://doi.org/10.1038/s41587-020-0591-3.