Package: Protein2Tissue 0.99.5

Chaoran Yang

Protein2Tissue: An R package for tissue expression analysis and gene set enrichment

Protein2Tissue provides a comprehensive framework for analysing tissue-specific gene and protein expression patterns. The package allows users to map genes or proteins to their predominant tissue types, perform tissue-based enrichment analysis on gene sets, and explore expression profiles across a wide range of human tissues. Reference expression data is derived from publicly available databases the Human Protein Atlas (https://www.proteinatlas.org).

Authors:Chaoran Yang [aut, cre], Yao Chen [aut]

Protein2Tissue_0.99.5.tar.gz
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Protein2Tissue_0.99.5.tgz(r-4.6-any)Protein2Tissue_0.99.5.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Protein2Tissue/json (API)

# Install 'Protein2Tissue' in R:
install.packages('Protein2Tissue', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/chryang/protein2tissue/issues

Datasets:
  • ee_tb - Human Protein Atlas tissue expression database
  • plasma_data - Example plasma proteomics dataset of age-associated protein expression
  • tissue_map - An example of the data frame the for the 'tissue_groups' parameter of 'geneClassification'.

On CRAN:

Conda:

proteomicstranscriptomicsgenesetenrichmentnetwork

2.48 score 3 scripts 13 exports 169 dependencies

Last updated from:447083eb25. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE259
linux-develWARNING352
source / vignettesERROR384
linux-releaseWARNING373
macos-releaseWARNING354
macos-oldrelWARNING339
windows-develWARNING287
windows-releaseWARNING292
windows-oldrelWARNING289
wasm-releaseOK181

Exports:geneClassificationgetBackgroundgetInputgoEnrichedheatmapEnrichnetworkPlotplotProteinTypeshowtestByTissuetestPlottissueAnalysistissueAnalysis2writeOutput

Dependencies:abindaisdkAnnotationDbiapeaplotaskpassbackportsbase64encBiobaseBiocBaseUtilsBiocGenericsBiostringsbitbit64blobbootbroombslibcachemcallrcarcarDatacliclusterclusterProfilercolorspacecorrplotcowplotcpp11crayoncurlDBIDerivdigestdoByDOSEdplyrenrichitenrichplotevaluateExactfarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforecastFormulafracdifffsgdtoolsgenericsggforceggfunggiraphggnewscaleggplot2ggplotifyggpubrggraphggrepelggsciggsignifggtangleggtreeglueGO.dbGOSemSimgraphlayoutsgridExtragridGraphicsgsongtablehighrhtmltoolshtmlwidgetshttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslorg.Hs.eg.dbotelpatchworkpbkrtestpillarpkgconfigplyrpngpolyclippolynomprocessxpspurrrquantregqvalueR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrmarkdownrootSolveRSQLiterstatixS4VectorsS7sassscalesscatterpieSeqinfoSparseMstringistringrsurvivalsyssystemfontstibbletidydrtidygraphtidyrtidyselecttidytreetimeDatetinytextreeiotweenrurcautf8vctrsviridisviridisLitewithrxfunXVectoryamlyulab.utilszoo