Registration and Call for Abstracts Open for Bioc2024

pram

Pooling RNA-seq datasets for assembling transcript models


Bioconductor version: Release (3.18)

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 (from within R, enter citation("pram")):

Installation

To install this package, start R (version "4.3") 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 PDF
NEWS Text

Details

biocViews BiologicalQuestion, GenePrediction, GenomeAnnotation, RNASeq, ResearchField, Sequencing, Software, Technology, Transcriptomics
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (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_1.18.0.tar.gz
Windows Binary pram_1.18.0.zip
macOS Binary (x86_64) pram_1.18.0.tgz
macOS Binary (arm64) pram_1.18.0.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