Package: clustermole 1.1.1.9000

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_1.1.1.9000.tar.gz
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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'))

Peer review:

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

On CRAN:

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

5.82 score 13 stars 34 scripts 480 downloads 5 exports 140 dependencies

Last updated 7 months agofrom:22099c5416. Checks:OK: 4 WARNING: 1 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winERRORNov 03 2024
R-4.5-linuxWARNINGNov 03 2024
R-4.4-winOKNov 03 2024
R-4.4-macERRORNov 03 2024
R-4.3-winOKNov 03 2024
R-4.3-macOKNov 03 2024

Exports:%>%clustermole_enrichmentclustermole_markersclustermole_overlapsread_gmt

Dependencies:abindannotateAnnotationDbiaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyredgeRevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegraphGSEABaseGSVAgtableHDF5ArrayhighrhtmltoolshtmlwidgetshttrIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcppreshapereshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdS4ArraysS4VectorssassScaledMatrixscalesSingleCellExperimentsingscoresnowSparseArraysparseMatrixStatsSpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc

Introduction to clustermole

Rendered fromclustermole-intro.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-05-06
Started: 2020-01-03