Tool Library list page for genomics topic with tag 'Gene transcripts'



5 tools

Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge.

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

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Stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome analysis.

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Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.

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An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.

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