DOI: 10.18129/B9.bioc.pram  

Pooling RNA-seq datasets for assembling transcript models

Bioconductor version: Release (3.18)

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

Author: Peng Liu [aut, cre], Colin N. Dewey [aut], Sündüz Keleş [aut]

Maintainer: Peng Liu <pliu55.wisc at>

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biocViews BiologicalQuestion, GenePrediction, GenomeAnnotation, RNASeq, ResearchField, Sequencing, Software, Technology, Transcriptomics
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 years)
License GPL (>= 3)
Depends R (>= 3.6)
Imports methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments(>= 1.16.0), rtracklayer(>= 1.40.6), BiocGenerics(>= 0.26.0), GenomeInfoDb(>= 1.16.0), GenomicRanges(>= 1.32.0), IRanges(>= 2.14.12), Rsamtools(>= 1.32.3), S4Vectors(>= 0.18.3)
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