Package: geneExpressionFromGEO 0.9
Davide Chicco
geneExpressionFromGEO: Easily Downloads a Gene Expression Dataset from a GEO Code and Retrieves the Gene Symbols of Its Probesets
A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, 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/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
Authors:
geneExpressionFromGEO_0.9.tar.gz
geneExpressionFromGEO_0.9.tar.gz(r-4.5-noble)geneExpressionFromGEO_0.9.tar.gz(r-4.4-noble)
geneExpressionFromGEO_0.9.tgz(r-4.4-emscripten)geneExpressionFromGEO_0.9.tgz(r-4.3-emscripten)
geneExpressionFromGEO.pdf |geneExpressionFromGEO.html✨
geneExpressionFromGEO/json (API)
# Install 'geneExpressionFromGEO' in R: |
install.packages('geneExpressionFromGEO', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davidechicco/geneexpressionfromgeo/issues
Last updated 3 years agofrom:5105112653. Checks:OK: 1 NOTE: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 13 2024 |
R-4.5-linux | NOTE | Dec 13 2024 |
Exports:dec_twogetGeneExpressionFromGEOreadUrl
Dependencies:abindannotateAnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicliprcommonmarkcpp11crayoncurldata.tableDBIDelayedArraydplyrfansifastmapgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOquerygluehmshttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclelimmamagrittrmarkdownMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsreadrrentrezrlangRSQLitervestS4ArraysS4VectorsselectrSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrxfunXMLxml2xtableXVectorzlibbioc