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pram

This is the development version of pram; for the stable release version, see pram.

Pooling RNA-seq datasets for assembling transcript models


Bioconductor version: Development (3.20)

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+bioconductor at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.21.1
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
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Suggests testthat, BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package pram_1.21.1.tar.gz
Windows Binary pram_1.21.0.zip
macOS Binary (x86_64) pram_1.21.1.tgz
macOS Binary (arm64) pram_1.21.0.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