ROGUE app is an R based web app with a graphic user interface that takes expression data as input such as raw read counts, length-normalized counts, expression units including fragments per kilobase of transcript per million mapped reads, reads per kilobase of transcript per million mapped reads (RPKM), and transcripts per million (TPM). Users can generate their own RNA-Seq matrix or download publicly available RNA-Seq expression data from databases such as gene expression omnibus, Array Express, The genotype tissue expression Project and the cancer genome atlas. When the input is raw read counts or length-normalized counts quantified by packages such as HT-seq or RSEM , ROGUE generates RPKM tables and can perform DEA using edgeR or DESeq2 which are two of the state-of-the-art R packages for DEA analysis and has been shown to outperform other methods in various applications . ROGUE also allows users to perform more advanced analyses such as biomarker discovery.

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