Package: SurfR 1.9.0

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_1.9.0.tar.gz
SurfR_1.9.0.zip(r-4.7)SurfR_1.9.0.zip(r-4.6)SurfR_1.9.0.zip(r-4.5)
SurfR_1.9.0.tgz(r-4.6-any)SurfR_1.9.0.tgz(r-4.5-any)
SurfR_1.9.0.tar.gz(r-4.7-any)SurfR_1.9.0.tar.gz(r-4.6-any)
SurfR_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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-1.9.0(bioc 3.24)SurfR-1.8.0(bioc 3.23)

softwaresequencingrnaseqgeneexpressiontranscriptiondifferentialexpressionprincipalcomponentgenesetenrichmentpathwaysbatcheffectfunctionalgenomicsvisualizationdataimportfunctionalpredictiongenepredictiongodgeenrichment-analysismetaanalysisplotsproteinspublic-datasurfacesurfaceome

5.26 score 6 stars 4 scripts 306 downloads 17 exports 173 dependencies

Last updated from:b697ac2b0c. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR239
linux-devel-x86_64WARNING450
source / vignettesOK373
linux-release-x86_64WARNING500
macos-release-arm64WARNING271
macos-oldrel-arm64WARNING227
windows-develWARNING344
windows-releaseWARNING360
windows-oldrelWARNING279
wasm-releaseOK209

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 May 27 2026.

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