Package: SurfR 1.1.0
SurfR: Surface Protein Prediction and Identification
Identify Surface Protein coding genes from a list of candidates. Systematically download data from GEO and TCGA or use your own data. Perform DGE on bulk RNAseq data. Perform Meta-analysis. Descriptive enrichment analysis and plots.
Authors:
SurfR_1.1.0.tar.gz
SurfR_1.1.0.tar.gz(r-4.5-noble)SurfR_1.1.0.tar.gz(r-4.4-noble)
SurfR_1.1.0.tgz(r-4.4-emscripten)SurfR_1.1.0.tgz(r-4.3-emscripten)
SurfR.pdf |SurfR.html✨
SurfR/json (API)
NEWS
# Install 'SurfR' in R: |
install.packages('SurfR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/auroramaurizio/surfr/issues
- countData - CountData
- enrichedList - EnrichedList
- ind_deg - Ind_deg
- metadata - Metadata
On BioConductor:SurfR-1.1.0(bioc 3.20)SurfR-1.0.0(bioc 3.19)
Last updated 2 months agofrom:b43b6d4286
Exports:Annotate_SPIDcombine_fisher_invnormDGEDownloadArchS4EnrichmentEnrichment_barplotenrichr_downloadGene2SProteinGEOmetadatametaRNAseqplotPCASplotSVennTCGA_download
Dependencies:abindade4admiscAnnotationDbiapeaskpassassertrbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocStylebiomaRtbiomformatBiostringsbitbit64blobbookdownbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2digestdoParalleldownloaderdplyrdynamicTreeCutedgeRenrichRevaluatefansifarverfastclusterfastmapfilelockfitdistrplusfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelglueGO.dbgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetaRNASeqmgcvmimemulttestmunsellmvtnormnlmennetopensslopenxlsxpermutephyloseqpillarpixmappkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloreadrreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrpartRSQLiterstudioapirvestS4ArraysS4VectorssassscalesselectrSingleCellExperimentsnowspSparseArraySPsimSeqstatmodstringistringrSummarizedExperimentsurvivalsysTCGAbiolinksTCGAbiolinksGUI.datatibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsveganvennviridisviridisLitevroomWGCNAwithrWriteXLSxfunXMLxml2XVectoryamlzipzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Annotate_SPID | Annotate_SPID |
combine_fisher_invnorm | combine_fisher_invnorm |
countData | countData |
DGE function | DGE |
DownloadArchS4 function | DownloadArchS4 |
enrichedList | enrichedList |
Enrichment function | Enrichment |
Enrichment_barplot | Enrichment_barplot |
Download data from enrichr in the form of a named list - function from hypeR | enrichr_download |
Gene2SProtein function | Gene2SProtein |
GEOmetadata function | GEOmetadata |
ind_deg | ind_deg |
metadata | metadata |
metaRNAseq function | metaRNAseq |
plotPCA function | plotPCA |
Splot function | Splot |
SVenn | SVenn |
TCGA_download function | TCGA_download |