Package: leo.sc 0.1.0

leo.sc: Layered Exploratory Omics (LEO for single-cell analysis)

LEO for single-cell analysis. This package provides useful functions for single-cell analysis workflow.

Authors:Ao Lu [aut, cre]

leo.sc_0.1.0.tar.gz
leo.sc_0.1.0.zip(r-4.7)leo.sc_0.1.0.zip(r-4.6)leo.sc_0.1.0.zip(r-4.5)
leo.sc_0.1.0.tgz(r-4.6-any)leo.sc_0.1.0.tgz(r-4.5-any)
leo.sc_0.1.0.tar.gz(r-4.7-any)leo.sc_0.1.0.tar.gz(r-4.6-any)
leo.sc_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
leo.sc/json (API)

# Install 'leo.sc' in R:
install.packages('leo.sc', repos = c('https://laleoarrow.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/laleoarrow/leo.sc/issues

Pkgdown/docs site:https://laleoarrow.github.io

On CRAN:

Conda:

geneticssingle-cell

4.20 score 1 stars 1 scripts 38 exports 220 dependencies

Last updated from:3e2d81c559. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE536
source / vignettesOK480
linux-release-x86_64NOTE567
macos-release-arm64NOTE396
macos-oldrel-arm64NOTE384
windows-develNOTE476
windows-releaseNOTE449
windows-oldrelNOTE451
wasm-releaseOK290

Exports:calcROGUEcheck_gene_avg_in_multi_batchcheck_gene_stats_in_multi_batchdoublet_rate_dictionarydoublet_removalfilter_clusters_by_percent_or_cell_countformat_markers_for_uploadget_cluster_countsgimme_markerleo_milo_visleo.augurleo.markerleo.miloleo.ROIElocate_most_different_g_in_2_groupmetadata_dropmetadata_get_colnamesmetadata_keepmetadata_write_10xplot_alluvialplot_alluvial_scplot_dbeeplot_gw_densityplot_highlight_clusterplot_qcplot_score_signature_heatmapread_sc_dataremove_unwant_hvgROIEscore_signatureseurat_basic_infoseurat_basic_qcseurat_standard_normalize_and_scalesilico_kosort_string_numeric_clusterssubset_common_gene_in_multi_batchsubset_srtwrite_10x_triple

Dependencies:abindaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbslibcachemCairocaToolscirclizecliclueclustercodetoolscoincolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdoParalleldotCall64DoubletFinderdplyrdqrngedgeRevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesGetoptLongggalluvialggbeeswarmggforceggplot2ggprismggraphggrastrggrepelggridgesggsciGlobalOptionsglobalsgluegoftestgplotsgraphlayoutsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrkslabelinglambda.rlaterlatticelazyevalleo.basiclibcoinlifecyclelimmalistenvlmtestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmiloRmimeminiUImodeltoolsmultcompmulticoolmvtnormNebulosanlmenortestnumDerivopensslotelparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclippracmaprogressrpromisespurrrR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterjsonrlangrmarkdownROCRROGUErprojrootRSpectrarsvdRtsneS4ArraysS4VectorsS7sandwichsassScaledMatrixscalesscattermoresctransformSeqinfoSeuratSeuratObjectshapeshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortextshapingTH.datatibbletidygraphtidyrtidyselecttinytextweenrutf8uwotvctrsviporviridisviridisLitewithrxfunxtableXVectoryamlzoo

Functional Inference Pipeline (FIP) DEMO

Rendered fromtutorial-sko.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-03-03
Started: 2026-03-02

Installation Guide

Rendered frominstallation.Rmdusingknitr::rmarkdownon May 19 2026.

Last update: 2026-03-03
Started: 2026-03-03

Readme and manuals

Help Manual

Help pageTopics
Calculate and plot ROGUE index for a Seurat object, with inline filteringcalcROGUE
Inspection of gene in multi-batchcheck_gene_avg_in_multi_batch check_gene_stats_in_multi_batch subset_common_gene_in_multi_batch
Lookup expected doublet rate based on cells loadeddoublet_rate_dictionary
Remove doublets using DoubletFinderdoublet_removal
Filter Seurat clusters by percentage or absolute cell countfilter_clusters_by_percent_or_cell_count
Format marker-gene lists for (bulk) uploadformat_markers_for_upload
Get cluster counts sorted descendingget_cluster_counts
Give me marker!gimme_marker
Visualize MiloR DA resultsleo_milo_vis
Run Augur analysisleo.augur
Marker hubleo.marker
Run Milo differential abundance workflow on a Seurat objectleo.milo
Compute Ro/e and draw heatmapleo.ROIE
Locate most distinguishing markers between two clusterslocate_most_different_g_in_2_group
Drop specified metadata columns from a Seurat objectmetadata_drop
Get specified metadata columns from a Seurat objectmetadata_get_colnames
Keep only selected metadata columns in a Seurat objectmetadata_keep
Export Seurat meta.data aligned to barcodesmetadata_write_10x
Draw alluvial bars with optional custom paletteplot_alluvial
Alluvial plot from a Seurat objectplot_alluvial_sc
Different-effect-variable Beeswarm Plotplot_dbee
Plot gene-weighted densityplot_gw_density
Highlight a clusterplot_highlight_cluster
Plot QC metricsplot_qc
Plot heatmap of signature scoresplot_score_signature_heatmap
Read single-cell data into a Seurat objectread_sc_data
Remove unwanted HVGsremove_unwant_hvg
Calculate ROIEROIE
Score sc_obj with signature listscore_signature
get basic summary of a seurat objectseurat_basic_info
Seurat basic QCseurat_basic_qc
Standard seurat normalize_and_scaleseurat_standard_normalize_and_scale
In-silico Knock-Out / Knock-In Analysis (single gene)silico_ko
Sort string-based cluster labels numerically and refactorsort_string_numeric_clusters
Subset srt obj easilysubset_srt
Export Seurat object to 10x-style triple fileswrite_10x_triple