Package: SurfR 1.7.0

Aurora Maurizio

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:Aurora Maurizio [aut, cre], Anna Sofia Tascini [aut, ctb]

SurfR_1.7.0.tar.gz
SurfR_1.7.0.zip(r-4.7)SurfR_1.7.0.zip(r-4.6)SurfR_1.7.0.zip(r-4.5)
SurfR_1.7.0.tgz(r-4.6-any)SurfR_1.7.0.tgz(r-4.5-any)
SurfR_1.7.0.tar.gz(r-4.6-any)SurfR_1.7.0.tar.gz(r-4.5-any)
SurfR_1.7.0.tgz(r-4.5-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

Datasets:

On BioConductor:SurfR-1.7.0(bioc 3.23)SurfR-1.6.0(bioc 3.22)

softwaresequencingrnaseqgeneexpressiontranscriptiondifferentialexpressionprincipalcomponentgenesetenrichmentpathwaysbatcheffectfunctionalgenomicsvisualizationdataimportfunctionalpredictiongenepredictiongodgeenrichment-analysismetaanalysisplotsproteinspublic-datasurfacesurfaceome

5.30 score 5 stars 4 scripts 280 downloads 17 exports 173 dependencies

Last updated from:90bbf06b83. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR256
linux-devel-x86_64NOTE557
source / vignettesOK485
linux-release-x86_64NOTE580
macos-release-arm64NOTE235
macos-oldrel-arm64NOTE415
windows-develNOTE347
windows-releaseNOTE374
windows-oldrelNOTE341
wasm-releaseOK546

Exports:Annotate_SPIDcombine_fisher_invnormDGEDownloadArchS4EnrichmentEnrichment_barplotenrichrenrichr_downloadGene2SProteinGEOmetadatalistEnrichrDbsmetaRNAseqplotPCAsetEnrichrSiteSplotSVennTCGA_download

Dependencies:abindade4admiscAnnotationDbiapeaskpassassertrbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocParallelbiomaRtbiomformatBiostringsbitbit64blobbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2digestdir.expirydoParalleldownloaderdplyrdynamicTreeCutedgeRevaluatefarverfastclusterfastmapfilelockfitdistrplusfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelgluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetaRNASeqmgcvmimemulttestmvtnormnlmennetopensslopenxlsxpermutephyloseqpillarpixmappkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloreadrreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrpartRSQLiterstudioapirvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoSingleCellExperimentsnowspSparseArraySPsimSeqstatmodstringistringrSummarizedExperimentsurvivalsysTCGAbiolinksTCGAbiolinksGUI.datatibbletidyrtidyselecttinytextzdbutf8vctrsveganvennviridisLitevroomWGCNAwithrxfunXMLxml2XVectoryamlzip

Introduction to SurfR

Aurora Maurizio, Anna Sofia Tascini, and Marco Jacopo Morelli

Rendered fromIntro_to_SurfR.Rmdusingknitr::rmarkdownon Apr 16 2026.

Last update: 2024-12-12
Started: 2022-12-05