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2. List of RNA-Seq bioinformatics tools | Wikipedia

   en.wikipedia.org/wiki/List_of_RNA-Seq...

   GENE-Counter is a Perl pipeline for RNA-Seq differential gene expression analyses. Gene-counter performs alignments with CASHX, Bowtie, BWA or other SAM output aligner. Differential gene expression is run with three optional packages (NBPSeq, edgeR and DESeq) using negative binomial distribution methods.