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bowtie

An ultrafast memory-efficient short read aligner

circtest

CircRNA testing and ploting R package

cufflinks

cummerbund

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/cummeRbund.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=cummeRbund.

dcc

htseq-tools

This repository hosts scripts and tools for analysis of high throughput sequencing data.

rna-seq_tuxedo

Using tophat, cufflinks, cuffmerge, and cuffdiff you can analyze your RNA-Seq data starting from fastq files. See Trapnell et al. 2014 for more information (http://www.nature.com/nprot/journal/v7/n3/abs/nprot.2012.016.html).

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

tophat

Spliced read mapper for RNA-Seq