Package: SurfR 1.3.6

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_1.3.6.tar.gz
SurfR_1.3.6.zip(r-4.5)SurfR_1.3.6.zip(r-4.4)SurfR_1.3.6.zip(r-4.3)
SurfR_1.3.6.tgz(r-4.5-any)SurfR_1.3.6.tgz(r-4.4-any)SurfR_1.3.6.tgz(r-4.3-any)
SurfR_1.3.6.tar.gz(r-4.5-noble)SurfR_1.3.6.tar.gz(r-4.4-noble)
SurfR_1.3.6.tgz(r-4.4-emscripten)SurfR_1.3.6.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

Datasets:

On BioConductor:SurfR-1.3.6(bioc 3.21)SurfR-1.2.6(bioc 3.20)

softwaresequencingrnaseqgeneexpressiontranscriptiondifferentialexpressionprincipalcomponentgenesetenrichmentpathwaysbatcheffectfunctionalgenomicsvisualizationdataimportfunctionalpredictiongenepredictiongodgeenrichment-analysismetaanalysisplotsproteinspublic-datasurfacesurfaceome

5.38 score 3 stars 3 scripts 122 downloads 17 exports 177 dependencies

Last updated 2 months agofrom:11a9df4591. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 30 2025
R-4.5-winNOTEJan 30 2025
R-4.5-macWARNINGJan 30 2025
R-4.5-linuxNOTEJan 30 2025
R-4.4-winNOTEJan 30 2025
R-4.4-macNOTEJan 30 2025
R-4.3-winNOTEJan 30 2025
R-4.3-macNOTEJan 30 2025

Exports:Annotate_SPIDcombine_fisher_invnormDGEDownloadArchS4EnrichmentEnrichment_barplotenrichrenrichr_downloadGene2SProteinGEOmetadatalistEnrichrDbsmetaRNAseqplotPCAsetEnrichrSiteSplotSVennTCGA_download

Dependencies:abindade4admiscAnnotationDbiapeaskpassassertrbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtbiomformatBiostringsbitbit64blobbslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2digestdoParalleldownloaderdplyrdynamicTreeCutedgeRevaluatefansifarverfastclusterfastmapfilelockfitdistrplusfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelglueGO.dbgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemetaRNASeqmgcvmimemulttestmunsellmvtnormnlmennetopensslopenxlsxpermutephyloseqpillarpixmappkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloreadrreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrpartRSQLiterstudioapirvestS4ArraysS4VectorssassscalesselectrSingleCellExperimentsnowspSparseArraySPsimSeqstatmodstringistringrSummarizedExperimentsurvivalsysTCGAbiolinksTCGAbiolinksGUI.datatibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsveganvennviridisviridisLitevroomWGCNAwithrxfunXMLxml2XVectoryamlzip

Introduction to SurfR

Aurora Maurizio, Anna Sofia Tascini, and Marco Jacopo Morelli

Rendered fromIntro_to_SurfR.Rmdusingknitr::rmarkdownon Jan 30 2025.

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