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:Davide Chicco [aut, cre]

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)

Peer review:

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

3 exports 0.23 score 88 dependencies 1 dependents 7 scripts 395 downloads

Last updated 3 years agofrom:5105112653. Checks:OK: 1 NOTE: 1. Indexed: yes.

Exports:dec_twogetGeneExpressionFromGEOreadUrl

Dependencies:abindannotateAnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicliprcommonmarkcpp11crayoncurldata.tableDBIDelayedArraydplyrfansifastmapgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOquerygluehmshttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclelimmamagrittrmarkdownMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsreadrrentrezrlangRSQLitervestS4ArraysS4VectorsselectrSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrxfunXMLxml2xtableXVectorzlibbioc