Digital gene expression data analysis software tools
Digital Gene Expression (DGE) is a cost-effective, sequence-based and quantitative 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. DGE software tools are used for mapping, parsing, annotation and analysis of RNA-seq and DGE data.
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 estimation, exact tests, generalized linear models and quasi likelihood tests. The package and methods are general, and can work on other sources of count data, such as barcoding experiments and peptide counts.
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 identifies possible unannotated ends de novo. It provides a robust handling of multi mapped reads, which is critical in 3’ DGE analysis. ESAT provides a module specifically designed for alternative start or 3’ UTR (untranslated region) differential isoform expression. It also includes a set of features specifically designed for the analysis of single-cell RNA-seq data.
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.
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, UniGene, and genomic DNA sequences to create a database of all tags that can be derived from a predefined restriction site. Next, it compares the experimental DGE tags to this tag database, taking advantage of the fact that the tags are stored as a prefix tree, or "trie", which allows for linear-time searches for exact matches. DGE tags with mismatches are analyzed by recursive calls in the data structure. We find that, in terms of alignment speed, the mapping functionality of trieFinder compares favorably with Bowtie.
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 a Perl software package for gene model renewal with DGE data.
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