Package: chevreulProcess 0.99.1
chevreulProcess: Tools for managing SingleCellExperiment objects as projects
Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.
Authors:
chevreulProcess_0.99.1.tar.gz
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chevreulProcess_0.99.1.tgz(r-4.4-any)
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chevreulProcess.pdf |chevreulProcess.html✨
chevreulProcess/json (API)
NEWS
# Install 'chevreulProcess' in R: |
install.packages('chevreulProcess', repos = c('https://whtns.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cobriniklab/chevreulprocess/issues
- cc.genes.cyclone - Cyclone cell cycle pairs by symbol
- ensembl_version - Ensembl version used for build
- grch38 - Human annotation data
- grch38_tx2gene - Human transcripts to genes
- human_to_mouse_homologs - Gene Homologs Between Human and Mouse
- small_example_dataset - Small example SingleCellExperiment
- tiny_sce - Tiny example SingleCellExperiment
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
Last updated 8 hours agofrom:21fcd9e9d2. Checks:ERROR: 5. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | FAIL | Oct 29 2024 |
R-4.5-win | ERROR | Oct 29 2024 |
R-4.5-linux | ERROR | Oct 29 2024 |
R-4.4-win | ERROR | Oct 29 2024 |
R-4.4-mac | ERROR | Oct 29 2024 |
Exports:add_percent_mitofind_all_markersgenes_to_transcriptsget_colDataget_feature_typesget_featuresget_sce_metadataget_variable_featuresintegration_workflowload_bigwigspropagate_spreadsheet_changesquery_experimentrecord_experiment_dataregress_cell_cyclereintegrate_scerename_sceretrieve_experimentsce_calcnsce_clustersce_desce_integratesce_preprocesssce_processset_colDataset_feature_typesplitByColstash_marker_featurestranscripts_to_genes
Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassassortheadbatchelorbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionBiostringsbitbit64bitopsblobblusterbriocachemCairocallrchevreuldatacirclizeclicliprclustercmdfuncodetoolscolorspacecowplotcpp11crayoncredentialscurlDBIdbplyrDelayedArrayDelayedMatrixStatsdescdiffobjdigestdplyrdqrngedgeREnhancedVolcanoEnrichmentBrowserEnsDb.Hsapiens.v86EnsDb.Mmusculus.v79ensembldbevaluateExperimentHubfansifarverfastmapfilelockFNNforcatsformatRfsfutile.loggerfutile.optionsfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgertggbeeswarmggplot2ggrastrggrepelghgitcredsGlobalOptionsglobalsglueGO.dbgraphgraphitegridExtraGSEABasegtableharmonyhmshttrhttr2hwriterigraphiniIRangesirlbaisobandjsonliteKEGGgraphKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmalistenvlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmegadepthmemoisemetapodmgcvmimemunsellnlmeopensslorg.Hs.eg.dbparallellypathviewpheatmappillarpkgbuildpkgconfigpkgloadplogrpngpraiseprettyunitsprocessxprogressProtGenericspspurrrR.methodsS3R.ooR.utilsR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRCurlreadrrematch2ResidualMatrixrestfulrRgraphvizRhpcBLASctlRhtslibrjsonrlangrprojrootRsamtoolsRSpectraRSQLiterstudioapirsvdrtracklayerRtsneS4ArraysS4VectorssafeScaledMatrixscalesscaterscranscuttleshapeSingleCellExperimentsitmosnowSparseArraySparseMsparseMatrixStatsSPIAstatmodstringistringrSummarizedExperimentsyssystemfontstestthattextshapingtibbletidyrtidyselecttzdbUCSC.utilsusethisutf8uwotvctrsviporviridisviridisLitevroomwaldowhiskerwithrxfunXMLxtableXVectoryamlzipzlibbioc