MPRAnalyze
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see MPRAnalyze.
Statistical Analysis of MPRA data
Bioconductor version: 3.18
MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.
Author: Tal Ashuach [aut, cre], David S Fischer [aut], Anat Kriemer [ctb], Fabian J Theis [ctb], Nir Yosef [ctb],
Maintainer: Tal Ashuach <tal_ashuach at berkeley.edu>
citation("MPRAnalyze")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MPRAnalyze")
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("MPRAnalyze")| Analyzing MPRA data with MPRAnalyze | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, CellBiology, Classification, DifferentialExpression, ExperimentalDesign, GeneExpression, ImmunoOncology, Sequencing, Software, StatisticalMethod |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | GPL-3 |
| Depends | |
| Imports | BiocParallel, methods, progress, stats, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/YosefLab/MPRAnalyze |
| Bug Reports | https://github.com/YosefLab/MPRAnalyze |
See More
| Suggests | knitr |
| 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 | MPRAnalyze_1.20.0.tar.gz |
| Windows Binary | MPRAnalyze_1.20.0.zip |
| macOS Binary (x86_64) | MPRAnalyze_1.20.0.tgz |
| macOS Binary (arm64) | MPRAnalyze_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MPRAnalyze |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MPRAnalyze |
| Bioc Package Browser | https://code.bioconductor.org/browse/MPRAnalyze/ |
| Package Short Url | https://bioconductor.org/packages/MPRAnalyze/ |
| Package Downloads Report | Download Stats |