README.md

In idot/deseq2analysis: DESeq2 analysis

DESEq2 Analysis wrapper

Usage

   deseq2analysis::analyseFromConfig("test.parameters.yaml", getwd())

It expects as input data in the yaml config (see example/test.parameters.yaml) * a tabular file with counts in columns per sample, genes in rows : countstable * a tabular sample description file : groupingtable * a tabular file specifying the comparisons done with the groupingtable groups : comparisonstable * a tabular file with the ENSEMBL info (geneid, gene_biotype, some_biotype, gene_name, gc, length) : ensembltable the ensembltable can be created with a python script, and will also be made optional

Example

there is a very small example/test dataset in example, and it has to be run from the example folder

   cd example
   ./rundemo.R

Important

deseq2analysis::analyseFromConfig the knitdir has to specified correctly in a singularity container its most often not getwd() ! its also better to specify all paths in the config file as absolute paths

idot/deseq2analysis documentation built on Aug. 14, 2021, 5:12 a.m.