Package: pram
Title: Pooling RNA-seq datasets for assembling transcript models
Version: 1.19.0
Authors@R: c(
    person( given="Peng",     family="Liu", email = "pliu55.wisc@gmail.com", 
            role = c("aut", "cre")),
    person( given="Colin N.", family="Dewey", role = c("aut")),
    person( given="Sündüz",   family="KeleĊŸ", 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
LazyData: true
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),
         GenomeInfoDb      (>= 1.16.0),
         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()'.