Package: pram
Title: Pooling RNA-seq datasets for assembling transcript models
Version: 1.28.0
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()'.
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:49:43 UTC
RemoteUrl: https://github.com/bioc/pram
RemoteRef: RELEASE_3_23
RemoteSha: f5011358c44a6eef7fc5d2db90d8f4e86ead8845
NeedsCompilation: no
Packaged: 2026-04-29 23:56:20 UTC; root
Author: Peng Liu [aut, cre],
  Colin N. Dewey [aut],
  Sündüz Keleş [aut]
Maintainer: Peng Liu <pliu55.wisc+bioconductor@gmail.com>
Built: R 4.6.0; ; 2026-04-30 01:31:45 UTC; unix
