MPRAnalyze

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

Statistical Analysis of MPRA data

Bioconductor version: Development (3.21)

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 (from within R, enter citation("MPRAnalyze")):

Installation

To install this package, start R (version "4.5") and enter:


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

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

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, CellBiology, Classification, DifferentialExpression, ExperimentalDesign, GeneExpression, ImmunoOncology, Sequencing, Software, StatisticalMethod
Version	1.25.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 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

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_1.25.0.tar.gz
Windows Binary (x86_64)	MPRAnalyze_1.25.0.zip (64-bit only)
macOS Binary (x86_64)	MPRAnalyze_1.25.0.tgz
macOS Binary (arm64)	MPRAnalyze_1.25.0.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