nf-core/geoquery/getgeo @ 0.0.0-3fc6d40
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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | c4ed7fdd281d290c622c5d93fa173effc0217fdb |
| Release Date | 22 Apr 2026 15:13:50 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgeoquery%2Fgetgeo/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/geoquery/getgeo/blobs/sha256:efbeb93a003196c59308dbf7156ddc68969cd887f7ddee0ba905799d69d870b1 |
| Size | 4.4 KB |
| Checksum | sha256:efbeb93a003196c59308dbf7156ddc68969cd887f7ddee0ba905799d69d870b1 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-c4ed7fd | 27 Apr 2026 15:00:16 (UTC) | 0 | 4.5 KB | |
| 0.0.0-6c4ed3a | 23 Apr 2026 15:21:17 (UTC) | 3 | 4.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:13:50 (UTC) | 3 | 4.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:05:55 (UTC) | 3 | 4.3 KB |