Package: clustermole 1.1.1

clustermole: Unbiased Single-Cell Transcriptomic Data Cell Type Identification

Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.

Authors:Igor Dolgalev [aut, cre]

clustermole_1.1.1.tar.gz
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clustermole_1.1.1.tgz(r-4.5-any)clustermole_1.1.1.tgz(r-4.4-any)clustermole_1.1.1.tgz(r-4.3-any)
clustermole_1.1.1.tar.gz(r-4.5-noble)clustermole_1.1.1.tar.gz(r-4.4-noble)
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clustermole.pdf |clustermole.html✨
clustermole/json (API)
NEWS

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

Bug tracker:https://github.com/igordot/clustermole/issues

Pkgdown site:https://igordot.github.io

On CRAN:

Conda:

cell-typecell-type-annotationcell-type-classificationcell-type-identificationcell-type-matchinggene-expression-signaturesscrna-seqsingle-cell

5.37 score 13 stars 36 scripts 444 downloads 5 exports 140 dependencies

Last updated 1 years agofrom:f343fa5e2d (on v1.1.1). Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winOKFeb 17 2025
R-4.5-macOKFeb 17 2025
R-4.5-linuxOKFeb 17 2025
R-4.4-winOKFeb 17 2025
R-4.4-macOKFeb 17 2025
R-4.3-winOKFeb 17 2025
R-4.3-macOKFeb 17 2025

Exports:%>%clustermole_enrichmentclustermole_markersclustermole_overlapsread_gmt

Dependencies:abindannotateAnnotationDbiaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyredgeRevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegraphGSEABaseGSVAgtableh5mreadHDF5ArrayhighrhtmltoolshtmlwidgetshttrIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcppreshapereshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdS4ArraysS4VectorssassScaledMatrixscalesSingleCellExperimentsingscoresnowSparseArraysparseMatrixStatsSpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryaml

Introduction to clustermole

Rendered fromclustermole-intro.Rmdusingknitr::rmarkdownon Feb 17 2025.

Last update: 2024-01-08
Started: 2020-01-03