TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data.

This protocol presents a state-of-the-art computational and statistical RNA-seq differential expression analysis workflow largely based on the free open-source R language and Bioconductor software ...

Sunetra Das *, Sharmishtha Shyamal †, David S. Durica †, Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems, Integrative and Comparative Biology, ...

Often the goal of a RNA-seq type experiment is to find differentially expressed genes. Below I give guidelines for calling differential expression. The major steps for differeatal expression are to ...

A cross-platform comparison of differential gene expression analysis. RNA-Seq is a powerful sequencing method that enables researchers to discover, profile and quantifyRNA transcripts across the ...