Package: EasyCellType 1.9.0

Ruoxing Li

EasyCellType: Annotate cell types for scRNA-seq data

We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.

Authors:Ruoxing Li [aut, cre, ctb], Ziyi Li [ctb]

EasyCellType_1.9.0.tar.gz
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EasyCellType.pdf |EasyCellType.html
EasyCellType/json (API)

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

On BioConductor:EasyCellType-1.9.0(bioc 3.21)EasyCellType-1.8.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecellsoftwaregeneexpressiongenesetenrichment

4.00 score 6 scripts 204 downloads 5 exports 133 dependencies

Last updated 5 months agofrom:902a85b14e. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 19 2025
R-4.5-winNOTEMar 19 2025
R-4.5-macNOTEMar 19 2025
R-4.5-linuxNOTEMar 19 2025
R-4.4-winNOTEMar 19 2025
R-4.4-macNOTEMar 19 2025
R-4.4-linuxNOTEMar 19 2025
R-4.3-winNOTEFeb 17 2025
R-4.3-macNOTEMar 19 2025

Exports:coremarkerseasyctplot_barplot_dotsummarycelltype

Dependencies:AnnotationDbiapeaplotaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiocStyleBiostringsbitbit64blobbookdownbslibcachemcliclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdigestDOSEdplyrenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgridGraphicsgsongtablehighrhtmltoolshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dborg.Mm.eg.dbpatchworkpillarpkgconfigplogrplyrpngpolyclippurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreshape2rlangrmarkdownRSQLiteS4VectorssassscalesscatterpiesnowstringistringrsyssystemfontstibbletidyrtidyselecttidytreetinytextreeiotweenrUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlyulab.utils

EasyCellType: an example workflow

Rendered frommy-vignette.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2022-06-28
Started: 2022-05-31