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:
clustermole_1.1.1.9000.tar.gz
clustermole_1.1.1.9000.zip(r-4.5)clustermole_1.1.1.9000.zip(r-4.4)clustermole_1.1.1.9000.zip(r-4.3)
clustermole_1.1.1.9000.tgz(r-4.4-any)clustermole_1.1.1.9000.tgz(r-4.3-any)
clustermole_1.1.1.9000.tar.gz(r-4.5-noble)clustermole_1.1.1.9000.tar.gz(r-4.4-noble)
clustermole_1.1.1.9000.tgz(r-4.4-emscripten)clustermole_1.1.1.9000.tgz(r-4.3-emscripten)
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
cell-typecell-type-annotationcell-type-classificationcell-type-identificationcell-type-matchinggene-expression-signaturesscrna-seqsingle-cell
Last updated 7 months agofrom:22099c5416. Checks:OK: 4 WARNING: 1 ERROR: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 03 2024 |
R-4.5-win | ERROR | Nov 03 2024 |
R-4.5-linux | WARNING | Nov 03 2024 |
R-4.4-win | OK | Nov 03 2024 |
R-4.4-mac | ERROR | Nov 03 2024 |
R-4.3-win | OK | Nov 03 2024 |
R-4.3-mac | OK | Nov 03 2024 |
Exports:%>%clustermole_enrichmentclustermole_markersclustermole_overlapsread_gmt
Dependencies:abindannotateAnnotationDbiaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiocSingularBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyredgeRevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegraphGSEABaseGSVAgtableHDF5ArrayhighrhtmltoolshtmlwidgetshttrIRangesirlbaisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlyplyrpngpromisespurrrR6rappdirsRColorBrewerRcppreshapereshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLitersvdS4ArraysS4VectorssassScaledMatrixscalesSingleCellExperimentsingscoresnowSparseArraysparseMatrixStatsSpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Cell types based on the expression of all genes | clustermole_enrichment |
Available cell type markers | clustermole_markers |
Cell types based on overlap of marker genes | clustermole_overlaps |
Read a GMT file into a data frame | read_gmt |