pram (original) (raw)

This is the released version of pram; for the devel version, seepram.

Pooling RNA-seq datasets for assembling transcript models

Bioconductor version: Release (3.20)

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+bioconductor at gmail.com>

Citation (from within R, enter citation("pram")):

Installation

To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pram")

For older versions of R, please refer to the appropriate Bioconductor release.

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browseVignettes("pram")

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