Pipeline askoR: User Guide

Susete Alves C., Kévin Gazengel, Fabrice Legeai
INRAE Centre Bretagne - Normandie, UMR 1349 IGEPP

ABSTRACT

RNAseq data analysis tool - AskoR
AskoR is an R pipeline for gene expression analysis from RNAseq data. It performs a complete and automatic transcriptomic analysis, through the articulation of well-known R packages (EdgeR, UpSetR, topGO, Coseq).
It includes theses steps:

• data filtering,
• normalisation of filtered data,
• descriptive analysis of data quality,
• differential gene expression analysis,
• enrichment in terms of "Gene Ontology",
• clustering genes by co-expression profile
• data synthesis from lists of genes

This package is also enriched with multiple graphic representations.

Table of contents:

• Required libraries
• Input files description
• Initialize and load data
• Filtering, Normalization and Correlation
• DE Analysis
• Basic comparisons
• GO Enrichment Analysis
• Co-Expression Analysis
• Tips and Tricks