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:
easyDifferentialGeneCoexpression_1.4.tar.gz
easyDifferentialGeneCoexpression_1.4.tar.gz(r-4.5-noble)easyDifferentialGeneCoexpression_1.4.tar.gz(r-4.4-noble)
easyDifferentialGeneCoexpression_1.4.tgz(r-4.4-emscripten)easyDifferentialGeneCoexpression_1.4.tgz(r-4.3-emscripten)
easyDifferentialGeneCoexpression.pdf |easyDifferentialGeneCoexpression.html✨
easyDifferentialGeneCoexpression/json (API)
| # Install 'easyDifferentialGeneCoexpression' in R: |
| install.packages('easyDifferentialGeneCoexpression', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davidechicco/easydifferentialgenecoexpression/issues
Last updated 8 months agofrom:81c51de92c. Checks:OK: 1 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 03 2024 |
| R-4.5-linux | ERROR | Sep 03 2024 |
Exports:easyDifferentialGeneCoexpressionfromProbesetToGeneSymbolgeoDataDownloadgeoPlatformAnnotationsDownloadprobesetRetrieval
Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbslibcachemcheckmateclicliprclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIDelayedArraydiffcoexpDiffCorrdigestdoParalleldplyrdynamicTreeCutevaluatefansifarverfastclusterfastmapfdrtoolfontawesomeforeachforeignFormulafsgeneExpressionFromGEOgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOqueryggplot2glueGO.dbGPArotationgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphimputeIRangesisobanditeratorsjetsetjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclelimmamagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemnormtmulttestmunsellnlmennetopensslorg.Hs.eg.dbpcaMethodspillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspsychpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrentrezrlangrmarkdownrpartRSQLiterstudioapirvestS4ArraysS4VectorssassscalesselectrSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisviridisLitevroomWGCNAwithrxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Function that computes the differential coexpression of a list of probesets in a specific dataset and returns the most significant pairs | easyDifferentialGeneCoexpression |
| Function that associates a gene symbol to a probeset for some Affymetrix platforms | fromProbesetToGeneSymbol |
| Function that downloads gene expression data from GEO, after checking the connection | geoDataDownload |
| Function that downloads the annotations of a GEO platform | geoPlatformAnnotationsDownload |
| Function that reads a CSV file of probesets or gene symbols and, in the latter case, it retrieves the original probesets | probesetRetrieval |