nf-core/geoquery/getgeo @ 0.0.0-0c7146d
Summary
Retrieves GEO data from the Gene Expression Omnibus (GEO)
Get started
Add the following snippet to your workflow script to include this module.
include { GEOQUERY_GETGEO } from 'nf-core/geoquery/getgeo'
License
MIT License
Process
Name
|
GEOQUERY_GETGEO |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing metadata about the GEO dataset, minimally 'id'. |
|---|---|
querygse
string
|
GSE identifier to pass to getGEO() |
Output
4 channels
#1
rds
tuple
meta
map
|
A Groovy map containing sample information |
|---|---|
*.rds
file
|
R object containing GEO data *.rds
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
#3
annotation
tuple
meta
map
|
A Groovy map containing sample information |
|---|---|
*annotation.tsv
file
|
TSV-format annotation file *annotation.tsv
|
#4
expression
tuple
meta
map
|
A Groovy map containing sample information |
|---|---|
*matrix.tsv
file
|
TSV-format expression matrix *matrix.tsv
|
| Tool | Description | Homepage |
|---|---|---|
| geoquery | Get data from NCBI Gene Expression Omnibus (GEO) | https://bioconductor.org/packages/release/bioc/html/GEOquery.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | e3e0c687eb5c129c011fca992af762ff2d4cb0f3 |
| Release Date | 08 Apr 2026 18:44:20 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgeoquery%2Fgetgeo/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/geoquery/getgeo/blobs/sha256:253d2043aab89de55878a679712f4de1fe2f4bfdfad2e37a8c338f2b4fa87d93 |
| Size | 4.3 KB |
| Checksum | sha256:253d2043aab89de55878a679712f4de1fe2f4bfdfad2e37a8c338f2b4fa87d93 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-e3e0c68 | 27 Apr 2026 21:15:37 (UTC) | 1 | 4.5 KB | ↔ | |
| 0.0.0-0c7146d | 08 Apr 2026 18:44:20 (UTC) | 1 | 4.3 KB | - |