pram

DOI: 10.18129/B9.bioc.pram  

Pooling RNA-seq datasets for assembling transcript models

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Pooling RNA-seq and Assembling Models
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, GenePrediction, GenomeAnnotation, RNASeq, ResearchField, Sequencing, Software, Technology, Transcriptomics
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 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)
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/pliu55/pram
BugReports	https://github.com/pliu55/pram/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pram_1.14.0.tar.gz
Windows Binary	pram_1.14.0.zip (64-bit only)
macOS Binary (x86_64)	pram_1.14.0.tgz
macOS Binary (arm64)	pram_1.14.0.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