pram
Pooling RNA-seq datasets for assembling transcript models
Bioconductor version: 3.23 · Package version: 1.28.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pram")Details
| Maintainer | Peng Liu <pliu55.wisc+bioconductor@gmail.com> |
| Author | Peng Liu [aut, cre], Colin N. Dewey [aut], Sündüz Keleş [aut] |
| License | GPL (>= 3) |
| URL | https://github.com/pliu55/pram |
| Bug Reports | https://github.com/pliu55/pram/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiologicalQuestion, GenePrediction, GenomeAnnotation, RNASeq, ResearchField, Sequencing, Software, Technology, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/pram/ |
Citation
From within R, enter citation("pram"):
Peng Liu, Colin N. Dewey, Sündüz Keleş. pram: Pooling RNA-seq datasets for assembling transcript models. doi:10.18129/B9.bioc.pram, R package version 1.28.0, https://bioconductor.org/packages/pram.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | pram_1.28.0.tar.gz |
| Windows binary (x86_64) | pram_1.28.0.zip |
| macOS binary (arm64) | pram_1.28.0.tgz |
| macOS binary (x86_64) | pram_1.28.0.tgz |
Dependencies
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)