pram
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see pram.
Pooling RNA-seq datasets for assembling transcript models
Bioconductor version: 3.11
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 "4.0") 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 | R Script | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | RNASeq, Sequencing, Software, Technology |
Version | 1.4.0 |
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_1.4.0.tar.gz |
Windows Binary | pram_1.4.0.zip |
macOS 10.13 (High Sierra) | pram_1.4.0.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 |
Old Source Packages for BioC 3.11 | Source Archive |