Package: scGOclust 0.2.1

Yuyao Song

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:Yuyao Song [aut, cre, ctb], Irene Papatheodorou [aut, ths]

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'))

Peer review:

Bug tracker:https://github.com/papatheodorou-group/scgoclust/issues

Datasets:
  • 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'

On CRAN:

5.50 score 9 stars 14 scripts 195 downloads 10 exports 179 dependencies

Last updated 9 months agofrom:d014f36903. Checks:OK: 6 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winOKNov 16 2024
R-4.5-linuxWARNINGNov 16 2024
R-4.4-winOKNov 16 2024
R-4.4-macOKNov 16 2024
R-4.3-winOKNov 16 2024
R-4.3-macOKNov 16 2024

Exports:analyzeGOSeuratcellTypeGOCorrcrossSpeciesCellTypeGOCorrensemblToGogetCellTypeGOgetCellTypeSharedGOgetCellTypeSharedTermsmakeGOSeuratplotCellTypeCorrHeatmapplotCellTypeSankey

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomefsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelimmalistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnetworkD3nlmeopensslparallellypatchworkpbapplypheatmappillarpkgconfigplogrplotlyplyrpngpolyclippracmaprettyunitsprogressprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRSQLiteRtsneS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinysitmoslantersourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstatmodstringistringrsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxml2xtableXVectoryamlzlibbioczoo

scGOclust_vignette

Rendered fromscGOclust_vignette.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2023-11-24
Started: 2023-09-30