🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

C++ API & command-line toolkit for working with BAM data

Application for making ENCODE Blacklists

SortMeRNA: next-generation sequence filtering and alignment tool

Fast, efficient RNA-Seq metrics for quality control and process optimization

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

SPP - R package for analysis of ChIP-seq and other functional sequencing data

Capturing protein-RNA interaction footprints from single-nucleotide CLIP-seq data

A collection of perl scripts for NGS analysis