Package: scPipeline 0.2.0.0
scPipeline: A Wrapper for 'Seurat' and Related R Packages for End-to-End Single Cell Analysis
Reports markers list, differentially expressed genes, associated pathways, cell-type annotations, does batch correction and other related single cell analyses all wrapped within 'Seurat'.
Authors:
scPipeline_0.2.0.0.tar.gz
scPipeline_0.2.0.0.tar.gz(r-4.5-noble)scPipeline_0.2.0.0.tar.gz(r-4.4-noble)
scPipeline_0.2.0.0.tgz(r-4.4-emscripten)
scPipeline.pdf |scPipeline.html✨
scPipeline/json (API)
NEWS
# Install 'scPipeline' in R: |
install.packages('scPipeline', repos = c('https://sridhara-omics.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 days agofrom:707dfc8239. Checks:3 OK. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 08 2025 |
R-4.5-linux | OK | Mar 08 2025 |
R-4.4-linux | OK | Mar 08 2025 |
Exports:AnnotateCellsWithSingleRConvertGeneIdentifiersReactomeDataSeuratLowDimSeuratMarkersSeuratPreprocessTransferAnnotations
Dependencies:abindalabaster.basealabaster.matrixalabaster.rangesalabaster.schemasalabaster.seAnnotationDbiAnnotationHubaskpassassortheadbase64encbatchelorbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionbiomaRtBiostringsbitbit64bitopsblobbslibcachemcaToolscelldexcliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngevaluateExperimentHubfansifarverfastDummiesfastmapfilelockfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsgypsumh5mreadHDF5Arrayherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2icaigraphIRangesirlbaisobandjquerylibjsonlitejsonvalidateKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenbaselifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprogressprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLReactomeGSAreshape2ResidualMatrixreticulaterhdf5rhdf5filtersRhdf5librlangrmarkdownROCRrprojrootRSpectraRSQLitersvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscattermoresctransformscuttleSeuratSeuratObjectshinySingleCellExperimentSingleRsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsutf8uwotV8vctrsviridisLitewithrxfunxml2xtableXVectoryamlzoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Annotate cells in a Seurat object using SingleR with Celldex | AnnotateCellsWithSingleR |
Convert Gene Identifiers in a Seurat Object | ConvertGeneIdentifiers |
Reactome Data Analysis for Seurat Object | ReactomeData |
Create a Low dimensional Seurat object from scaled seurat object | SeuratLowDim |
A thresholded markers list for better calculation of DE genes | SeuratMarkers |
Preprocess count data and create a Seurat object | SeuratPreprocess |
Transfer annotations to Seurat clusters | TransferAnnotations |