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]

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clustermole.pdf |clustermole.html✨
clustermole/json (API)
NEWS

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 exports 13 stars 1.83 score 139 dependencies 32 scripts 595 downloads

Last updated 4 months agofrom:22099c5416. Checks:OK: 6 ERROR: 1. Indexed: yes.

Exports:%>%clustermole_enrichmentclustermole_markersclustermole_overlapsread_gmt

Dependencies:abindannotateAnnotationDbiaskpassbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyredgeRevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegraphGSEABaseGSVAgtableHDF5ArrayhighrhtmltoolshtmlwidgetshttrIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcppreshapereshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdS4ArraysS4VectorssassScaledMatrixscalesSingleCellExperimentsingscoresnowSparseArraysparseMatrixStatsSpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc