pram
Pooling RNA-seq datasets for assembling transcript models
Bioconductor version: Release (3.19)
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.
Author: Peng Liu [aut, cre], Colin N. Dewey [aut], Sündüz Keleş [aut]
Maintainer: Peng Liu <pliu55.wisc at gmail.com>
citation("pram")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pram")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pram")| Pooling RNA-seq and Assembling Models | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, GenePrediction, GenomeAnnotation, RNASeq, ResearchField, Sequencing, Software, Technology, Transcriptomics |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | GPL (>= 3) |
| 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) |
| System Requirements | |
| URL | https://github.com/pliu55/pram |
| Bug Reports | https://github.com/pliu55/pram/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pram_1.20.0.tar.gz |
| Windows Binary (x86_64) | pram_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | pram_1.20.0.tgz |
| macOS Binary (arm64) | pram_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pram |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pram |
| Bioc Package Browser | https://code.bioconductor.org/browse/pram/ |
| Package Short Url | https://bioconductor.org/packages/pram/ |
| Package Downloads Report | Download Stats |