MBASED
This is the released version of MBASED; for the devel version, see MBASED.
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
Bioconductor version: Release (3.23)
The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.
Author: Oleg Mayba, Houston Gilbert
Maintainer: Oleg Mayba <mayba.oleg at gene.com>
citation("MBASED")):
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")
BiocManager::install("MBASED")
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("MBASED")| MBASED | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Sequencing, Software, Transcription |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | Artistic-2.0 |
| Depends | RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle |
| 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 | MBASED_1.46.0.tar.gz |
| Windows Binary (x86_64) | MBASED_1.46.0.zip |
| macOS Binary (big-sur-x86_64) | MBASED_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | MBASED_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MBASED |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MBASED |
| Bioc Package Browser | https://code.bioconductor.org/browse/MBASED/ |
| Package Short Url | https://bioconductor.org/packages/MBASED/ |
| Package Downloads Report | Download Stats |