BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specifi

EPIC is a R package and Shiny app to estimate the proportions of different cell types from bulk gene expression data.

Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference g

Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference g

A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. I

A tool for transcript expression quantification from RNA-seq data

A tool for transcript expression quantification from RNA-seq data

This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM f

This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM f

Ultrafast universal RNA-seq aligner. Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately

Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de

Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called

A package that provides tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular