Welcome to the Geo Array Digest resource, or “GAD” for short!
Geo Array Digest (GAD) resource is an automated messaging service that monitors available of public array datasets made available in GEO database. The GAD service was constructed by scheduling queries to the GEO API using the Entrez Programming Utilities software. Automated status updates to the GAD Bot Twitter account are made using the twitteR R package in a snakemake workflow. It is maintained by Sean Maden, PhD (GitHub: metamaden, Twitter: @MadenSean).
The digest targets a handful of the most numerous or active platforms on GEO. Details about the array platforms included in digests are provided in the manifest table at ~/data/arraymetadf.csv. The current version of the array platforms manifest looks like this:
| accession | alias | type | description | release_date | spp |
|---|---|---|---|---|---|
| GPL13534 | Illumina Infinium HM450 BeadChip | DNAm | Major array platform probing DNA methylation at roughly 480k CpG loci. | 13-May-11 | human |
| GPL21145 | Illumina Infinium EPIC/HM850 BeadChip | DNAm | Major array platform probing DNA methylation at roughly 850k CpG loci. | 16-Nov-15 | human |
| GPL570 | Affymetrix Human Genome U133 Plus 2.0 Array | expression | Major human gene expression/transcript profiling array using oligonucleotide assays. | 3-Nov-03 | human |
| GPL10558 | Illumina HumanHT-12 V4.0 expression beadchip | expression | Major human gene expression/transcript profiling array using oligonucleotide beads. | 17-Jan-10 | human |
| GPL96 | Affymetrix Human Genome U133A Array | expression | Major human gene expression/transcript profiling array using oligonucleotide assays. | 3/11/02 | human |
For platform GPL13534 (HM450K), found 1594 studies and 112586 samples. Of these, 824 studies and 58180 samples have IDATs.
For platform GPL13534 (HM450K), found 1594 studies and 112586 samples. Of these, 824 studies and 58180 samples have IDATs.
For platform GPL13534 (HM450K), found 1594 studies and 112586 samples. Of these, 824 studies and 58180 samples have IDATs.
For platform GPL13534 (HM450K), found 1594 studies and 112586 samples. Of these, 824 studies and 58180 samples have IDATs.
For platform GPL13534 (HM450K), found 1594 studies and 112586 samples.. Of these, 824 studies and 58180 samples have IDATs.