MPRAnalyze

DOI: 10.18129/B9.bioc.MPRAnalyze    

Statistical Analysis of MPRA data

Bioconductor version: Release (3.8)

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], Nir Yosef [ctb], Fabian J Theis [ctb],

Maintainer: Tal Ashuach <tal_ashuach at berkeley.edu>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MPRAnalyze", version = "3.8")

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")

 

HTML R Script Analyzing MPRA data with MPRAnalyze
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, Sequencing, Software, StatisticalMethod
Version 1.0.0
License GPL-3
Depends
Imports BiocParallel, methods, progress, stats, SummarizedExperiment
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL https://github.com/YosefLab/MPRAnalyze
BugReports https://github.com/YosefLab/MPRAnalyze
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MPRAnalyze_1.0.0.tar.gz
Windows Binary MPRAnalyze_1.0.0.zip
Mac OS X 10.11 (El Capitan) MPRAnalyze_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MPRAnalyze
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MPRAnalyze
Package Short Url http://bioconductor.org/packages/MPRAnalyze/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: