Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
Define where the pipeline should find input data and save output data.
Ways of providing your abundance values
Options related to features
Options for processing of affy arrays with justRMA()
Options for processing of proteomics MaxQuant tables with the Proteus R package
Options related to filtering upstream of differential analysis
Options related to data exploration
Options related to differential operations
Reference genome related files and options required for the workflow.
Parameters used to describe centralised config profiles. These should not be edited.
Set the top limit for requested resources for any single job.
Less common options for the pipeline, typically set in a config file.