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Digital gene expression data analysis bioinformatics software tools

Digital Gene Expression (DGE) is a cost-effective, sequence-based approach for simple transcript quantification: by sequencing one read per molecule of RNA, this technique can be used to efficiently count transcripts while obviating the need for…
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ESAT
Desktop

ESAT End Sequence Analysis ToolKit

A toolkit designed for the analysis of short reads obtained from end-sequence…

A toolkit designed for the analysis of short reads obtained from end-sequence RNA-seq. ESAT addresses mis-annotated or sample-specific transcript boundaries by providing a search step in which it…

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digitagCT
Desktop

digitagCT

An integrated bioinformatics approach that combines DGE tags, RNA-Seq, tiling…

An integrated bioinformatics approach that combines DGE tags, RNA-Seq, tiling array expression data and species-comparison to explore new transcriptional regions and their specific biological…

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edgeR
Desktop

edgeR empirical analysis of DGE in R

Allows differential expression analysis of digital gene expression data. edgeR…

Allows differential expression analysis of digital gene expression data. edgeR implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes…

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trieFinder
Desktop

trieFinder

A program specifically designed to rapidly map, parse, and annotate DGE tags of…

A program specifically designed to rapidly map, parse, and annotate DGE tags of various lengths against cDNA and/or genomic sequence databases. The trieFinder algorithm maps DGE tags in a two-step…

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Gene2DGE
Desktop

Gene2DGE

More and more digital gene expression (DGE) scannings have indicated the…

More and more digital gene expression (DGE) scannings have indicated the presence of huge amount of novel transcripts in addition to the known gene models. However, almost all these studies still…

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