Runs a differential expression analysis with dream() from variancePartition R package
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
(Mandatory) 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’.
limma::makeContrasts
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.
results
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
model
Metadata map passed through from input.
*.dream.model.txt:file
R model description text file.
*.dream.model.txt
versions
versions.yml:file
File containing software versions
versions.yml
Differential expression for repeated measures
