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 and reducing the total numbers of reads necessary for accurate quantification. Source text: Renaud et al., 2014.
digitagCT
digitagCT
An integrated bioinformatics approach that combines DGE tags, RNA-Seq, tiling array…
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 features, particularly tissue expression or conservation.
edgeR
edgeR
Differential expression analysis of RNA-seq and digital gene expression profiles with…
Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis…
Gene2DGE
Gene2DGE
More and more digital gene expression (DGE) scannings have indicated the presence of huge…
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 depend crucially on existing annotation. Gene2DGE is…
trieFinder
trieFinder
A program specifically designed to rapidly map, parse, and annotate DGE tags of various…
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 process. First, it scans FASTA files of RefSeq,…