Package: easyDifferentialGeneCoexpression 1.4

Davide Chicco

easyDifferentialGeneCoexpression: Easily Performs Differential Coexpression Analysis

A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

Authors:Davide Chicco [aut, cre]

easyDifferentialGeneCoexpression_1.4.tar.gz
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easyDifferentialGeneCoexpression_1.4.tgz(r-4.5-any)easyDifferentialGeneCoexpression_1.4.tgz(r-4.4-any)easyDifferentialGeneCoexpression_1.4.tgz(r-4.3-any)
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easyDifferentialGeneCoexpression.pdf |easyDifferentialGeneCoexpression.html✨
easyDifferentialGeneCoexpression/json (API)

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

Bug tracker:https://github.com/davidechicco/easydifferentialgenecoexpression/issues

On CRAN:

archivedpackagesr-universe

2.70 score 5 stars 2 scripts 217 downloads 5 exports 151 dependencies

Last updated 7 days agofrom:05a49c08db (on package/easyDifferentialGeneCoexpression). Checks:8 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 13 2025
R-4.5-winOKFeb 13 2025
R-4.5-macOKFeb 13 2025
R-4.5-linuxOKFeb 13 2025
R-4.4-winOKFeb 13 2025
R-4.4-macOKFeb 13 2025
R-4.3-winOKFeb 13 2025
R-4.3-macOKFeb 13 2025

Exports:easyDifferentialGeneCoexpressionfromProbesetToGeneSymbolgeoDataDownloadgeoPlatformAnnotationsDownloadprobesetRetrieval

Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbslibcachemcheckmateclicliprclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIDelayedArraydiffcoexpDiffCorrdigestdoParalleldplyrdynamicTreeCutevaluatefansifarverfastclusterfastmapfdrtoolfontawesomeforeachforeignFormulafsgeneExpressionFromGEOgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOqueryggplot2glueGO.dbGPArotationgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphimputeIRangesisobanditeratorsjetsetjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclelimmamagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemnormtmulttestmunsellnlmennetopensslorg.Hs.eg.dbpcaMethodspillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspsychpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrentrezrlangrmarkdownrpartRSQLiterstudioapirvestS4ArraysS4VectorssassscalesselectrSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisviridisLitevroomWGCNAwithrxfunXMLxml2xtableXVectoryaml

easyDifferentialGeneCoexpression

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Last update: 2025-02-13
Started: 2025-02-13