Nextflow Registry | nf-core/variancepartition/dream@0.0.0-0c7146d

nf-core/variancepartition/dream @ 0.0.0-0c7146d

Runs a differential expression analysis with dream() from variancePartition R package

rnaseq dream variancepartition

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @alanmmobbs03 @nschcolnicov @atrigila

Maintainers: @alanmmobbs03 @nschcolnicov @atrigila

Runs a differential expression analysis with dream() from variancePartition R package

Add the following snippet to your workflow script to include this module.

include { VARIANCEPARTITION_DREAM } from 'nf-core/variancepartition/dream'

MIT License

Process

`Name`	`VARIANCEPARTITION_DREAM`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing run and contrast information.
`contrast_variable` string	The column in the sample sheet that should be used to define groups for comparison
`reference` string	The value within the contrast_variable column of the sample sheet that should be used to derive the reference samples
`target` string	The value within the contrast_variable column of the sample sheet that should be used to derive the target samples
`formula` string	(Optional) R formula string used for modeling, e.g. '~ treatment + (1 \| sample_number)'.
`comparison` string	(Optional) Literal string passed to `limma::makeContrasts`, e.g. 'treatmenthND6 - treatmentmCherry'.

#2 tuple

`meta2` map	Groovy map containing study-wide metadata related to the sample sheet and matrix
`samplesheet` file	Sample sheet file containing sample metadata.
`counts` file	TSV or CSV format expression matrix with genes as rows and samples as columns.

Output 4 channels

#1 model tuple

`meta` map	groovy array with metadata information for the contrast generated
`*.dream.model.txt` file	R model description text file. `*.dream.model.txt`

#2 results tuple

`meta` map	groovy array with metadata information for the contrast generated
`*.dream.results.tsv` file	TSV-format table of differential expression information as output by Dream `*.dream.results.tsv`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

#4 normalised_counts tuple

`meta` map	groovy array with metadata information for the contrast generated
`*.normalised_counts.tsv` file	normalised TSV format expression matrix with genes by row and samples by column `*.normalised_counts.tsv`

Tool	Description	Homepage
dream	Differential expression for repeated measures	https://www.bioconductor.org/packages/release/bioc/html/variancePartition.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:21:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvariancepartition%2Fdream/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/variancepartition/dream/blobs/sha256:ea9945f334e09d9c653d37b613cc563b185b304e75784bccb121d4a09545e777
Size	9.0 KB
Checksum	sha256:ea9945f334e09d9c653d37b613cc563b185b304e75784bccb121d4a09545e777
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:21:10 (UTC)		1	9.0 KB