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URL: http://sourceforge.net/projects/pennseq/
Proper Citation: PennSeq (RRID:SCR_001763)
Description: Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.
Abbreviations: PennSeq
Resource Type: software resource
Defining Citation: PMID:24362841
Keywords: isoform, gene expression, rna-seq, bio.tools
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