Package: scGOclust 0.2.1
scGOclust: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq
Traditional methods for analyzing single cell RNA-seq datasets focus solely on gene expression, but this package introduces a novel approach that goes beyond this limitation. Using Gene Ontology terms as features, the package allows for the functional profile of cell populations, and comparison within and between datasets from the same or different species. Our approach enables the discovery of previously unrecognized functional similarities and differences between cell types and has demonstrated success in identifying cell types' functional correspondence even between evolutionarily distant species.
Authors:
scGOclust_0.2.1.tar.gz
scGOclust_0.2.1.zip(r-4.5)scGOclust_0.2.1.zip(r-4.4)scGOclust_0.2.1.zip(r-4.3)
scGOclust_0.2.1.tgz(r-4.4-any)scGOclust_0.2.1.tgz(r-4.3-any)
scGOclust_0.2.1.tar.gz(r-4.5-noble)scGOclust_0.2.1.tar.gz(r-4.4-noble)
scGOclust_0.2.1.tgz(r-4.4-emscripten)
scGOclust.pdf |scGOclust.html✨
scGOclust/json (API)
# Install 'scGOclust' in R: |
install.packages('scGOclust', repos = c('https://papatheodorou-group.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/papatheodorou-group/scgoclust/issues
- dme_subset - Drosophila gut scRNA-seq data, 10X Chromium Subset to 45 cells per cell type as an example data
- dme_tbl - Drosophila EMSEMBL gene and GO annotation, subset to genes present in 'dme_subset'
- mmu_subset - Mouse stomach and intestine scRNA-seq data, microwell-seq Subset to 50 cells per cell type as an example data
- mmu_tbl - Mouse EMSEMBL gene and GO annotation, subset to genes present in 'mmu_subset'
Last updated 9 months agofrom:d014f36903. Checks:OK: 6 WARNING: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 16 2024 |
R-4.5-win | OK | Nov 16 2024 |
R-4.5-linux | WARNING | Nov 16 2024 |
R-4.4-win | OK | Nov 16 2024 |
R-4.4-mac | OK | Nov 16 2024 |
R-4.3-win | OK | Nov 16 2024 |
R-4.3-mac | OK | Nov 16 2024 |
Exports:analyzeGOSeuratcellTypeGOCorrcrossSpeciesCellTypeGOCorrensemblToGogetCellTypeGOgetCellTypeSharedGOgetCellTypeSharedTermsmakeGOSeuratplotCellTypeCorrHeatmapplotCellTypeSankey
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelimmalistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnetworkD3nlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplogrplotlyplyrpngpolyclippracmaprettyunitsprogressprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRSQLiteRtsneS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinysitmoslantersourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxml2xtableXVectoryamlzlibbioczoo