Package: ASURAT 1.9.0
ASURAT: Functional annotation-driven unsupervised clustering for single-cell data
ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
Authors:
ASURAT_1.9.0.tar.gz
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ASURAT.pdf |ASURAT.html✨
ASURAT/json (API)
NEWS
# Install 'ASURAT' in R: |
install.packages('ASURAT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- human_COMSig_eg - A list of small Cell Ontology and MSigDB databases for human.
- human_GO_eg - A list of small Gene Ontology database for human.
- human_KEGG_eg - A list of small KEGG database for human.
- pbmc_eg - A SingleCellExperiment object made from a gene expression table.
- pbmcs_eg - A list of SingleCellExperiment objects made from sign-sample matrices.
On BioConductor:ASURAT-1.9.0(bioc 3.20)ASURAT-1.8.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:8cc0b56f5c
Exports:add_metadatabubble_sortcluster_genesetscompute_sepI_allcompute_sepI_clusterscreate_signsmakeSignMatrixplot_dataframe3Dplot_multiheatmapsremove_samplesremove_signsremove_signs_manuallyremove_signs_redundantremove_variablesremove_variables_secondselect_signs_manuallyswap_pass
Dependencies:abindaskpassBiobaseBiocGenericscirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayoncurlDelayedArraydigestdoParallelforeachGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongGlobalOptionshttrIRangesiteratorsjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimemisc3dopensslplot3DpngR6RColorBrewerRcpprjsonS4ArraysS4VectorsshapeSingleCellExperimentSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc