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 (3.24)
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("pram")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, GenePrediction, GenomeAnnotation, RNASeq, ResearchField, Sequencing, Software, Technology, Transcriptomics |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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), Seqinfo, 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | pram_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | pram_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | pram_1.29.0.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 |