From: First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
Tool | R | Local | GUI | GEO | AE | SRA | DB | ANN | Search | Note |
---|---|---|---|---|---|---|---|---|---|---|
COMMAND>_ | NO | YES | YES | YES | YES | YES | YES | YES | YES | |
GEOquery | YES | NO | NO | YES | NO | NO | NO | NO | NO | |
ArrayExpress | YES | NO | NO | NO | YES | NO | NO | NO | YES | |
GEOmetadb | YES | NO | NO | YES | NO | YES | NO | NO | YES | requires the dowload of an sqlite file with meta information |
SRAdb | YES | NO | NO | YES | NO | YES | NO | NO | YES | requires the dowload of an sqlite file with meta information |
compendiumdb | YES | NO | NO | YES | NO | NO | YES | NO | NO | |
virtualArray | YES | YES | NO | YES | YES | NO | NO | NO | NO | allow to normalize data and correct for batch effect, available only for Bioconductor <= 2.14 |
Microarray retriever | NO | NO | YES | YES | YES | NO | YES | NO | YES | unavailable |