Package: TissueEnrich 1.25.1

Ashish Jain

TissueEnrich: Tissue-specific gene enrichment analysis

The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.

Authors:Ashish Jain [aut, cre], Geetu Tuteja [aut]

TissueEnrich_1.25.1.tar.gz
TissueEnrich_1.25.1.zip(r-4.5)TissueEnrich_1.25.1.zip(r-4.4)TissueEnrich_1.25.1.zip(r-4.3)
TissueEnrich_1.25.1.tgz(r-4.4-any)TissueEnrich_1.25.1.tgz(r-4.3-any)
TissueEnrich_1.25.1.tar.gz(r-4.5-noble)TissueEnrich_1.25.1.tar.gz(r-4.4-noble)
TissueEnrich_1.25.1.tgz(r-4.4-emscripten)TissueEnrich_1.25.1.tgz(r-4.3-emscripten)
TissueEnrich.pdf |TissueEnrich.html✨
TissueEnrich/json (API)
NEWS

Peer review:

On BioConductor:TissueEnrich-1.25.1(bioc 3.20)TissueEnrich-1.24.1(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

3 exports 3.19 score 79 dependencies 18 mentions

Last updated 2 months agofrom:195feb6319

Exports:teEnrichmentteEnrichmentCustomteGeneRetrieval

Dependencies:abindannotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIDelayedArraydplyrfansifarverfastmapgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphGSEABasegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngpurrrR6RColorBrewerrlangRSQLiteS4ArraysS4VectorsscalesSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVectorzlibbioc