RNA-Seq analysis Tools

R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

Genomic Mapping and Alignment Program for mRNA and EST Sequences.

IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores.

IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique.

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome.

Megadepth is a fast tool for computing coverage and quantifying alignments from BAM and BigWig files, designed for large-scale genomic and transcriptomic analyses with support for junction coverage and annotation-based quantification.

The goal of metaseq is to tie together lots of existing software into a framework for exploring genomic data. It focuses on flexibility and interactive exploration and plotting of disparate genomic data sets.

Program for comparing, annotating, merging and tracking transcripts in GFF files.

Program for filtering, converting and manipulating GFF files

Command line tool to annotate with a standard naming miRNAs e isomiRs.