Package: pram
Title: Pooling RNA-seq datasets for assembling transcript models
Version: 1.29.0
Authors@R: c(
    person( given="Peng",     family="Liu",
            email = "pliu55.wisc+bioconductor@gmail.com",
            role = c("aut", "cre")),
    person( given="Colin N.", family="Dewey", role = c("aut")),
    person( given="Sündüz",   family="Keleş", role = c("aut")) )
Description: 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.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/pliu55/pram
BugReports: https://github.com/pliu55/pram/issues
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), Seqinfo, GenomicRanges (>= 1.32.0),
        IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>=
        0.18.3)
RoxygenNote: 6.1.0
Suggests: testthat, BiocStyle, knitr, rmarkdown
Collate: 'Param.R' 'Transcript.R' 'buildModel.R' 'defIgRanges.R'
        'evalModel.R' 'prepIgBam.R' 'runPRAM.R' 'selModel.R' 'util.R'
VignetteBuilder: knitr
biocViews: Software, Technology, Sequencing, RNASeq,
        BiologicalQuestion, GenePrediction, GenomeAnnotation,
        ResearchField, Transcriptomics
SystemsRequirements: buildModel() and runPRAM() functions require
        external software Cufflinks, StringTie, and/or TACO. For
        details, please see the 'Required external software' section in
        vignette's 'Building transcript models: buildModel()'.
git_url: https://git.bioconductor.org/packages/pram
git_branch: devel
git_last_commit: e06acb5
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.24
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-29 00:24:16 UTC; biocbuild
Author: Peng Liu [aut, cre],
  Colin N. Dewey [aut],
  Sündüz Keleş [aut]
Maintainer: Peng Liu <pliu55.wisc+bioconductor@gmail.com>
