Package: pram 1.21.1
Peng Liu
pram: Pooling RNA-seq datasets for assembling transcript models
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.
Authors:
pram_1.21.1.tar.gz
pram_1.21.1.zip(r-4.5)pram_1.21.1.zip(r-4.4)pram_1.21.1.zip(r-4.3)
pram_1.21.1.tgz(r-4.4-any)pram_1.21.1.tgz(r-4.3-any)
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pram_1.21.1.tgz(r-4.4-emscripten)pram_1.21.1.tgz(r-4.3-emscripten)
pram.pdf |pram.html✨
pram/json (API)
NEWS
| # Install 'pram' in R: |
| install.packages('pram', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pliu55/pram/issues
On BioConductor:pram-1.21.0(bioc 3.20)pram-1.20.0(bioc 3.19)
Last updated 28 days agofrom:79fcd4d2e7
Exports:buildModeldefIgRangesevalModelprepIgBamrunPRAMselModel
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurldata.tableDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build transcript models from aligned RNA-seq data | buildModel |
| Define intergenic genomic regions | defIgRanges |
| Evaluate transcript model | evalModel evalModel,character,character-method evalModel,character,data.table-method evalModel,data.table,data.table-method evalModel,GRanges,GRanges-method |
| Extract alignments in intergenic regions from BAM files | prepIgBam |
| Predict intergenic transcript models from RNA-seq | runPRAM |
| Select transcript models | selModel |
