- cutadapt, for trimming reads
- STAR aligner, for aligning reads to a reference
- htseq-count, for quantifying read counts at genomic features
- Picard tools, including CollectRnaSeqMetrics
- FastQC, for basic FASTQ quality control
- MultiQC, for aggregating quality control reports
- DESeq2, original manuscript: Love et al, 2014
- tximport, original manuscript: Soneson et al, 2014
- edgeR, original manuscript: Robinson et al, 2010
- limma, original manuscript: Ritchie et al, 2015
- limma-voom