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 transcript-length normalization…
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edgeR
Desktop

edgeR

A package to dampen the effect of outliers on count-based differential…

A package to dampen the effect of outliers on count-based differential expression analyses. edgeR uses empirical Bayes estimation and exact tests based on the negative binomial distribution and is…

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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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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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