README.md

In lux2ht/mpraprofiler: Statistical Analysis and Visualization for MPRA Data

mpraprofiler

The goal of mpraprofiler is to create a simple tool to perform allelic differential expression analysis for massively parallel reporter assay (MPRA) data.

This is still a developing version. No class has been defined.

Installation

You can install mpraprofiler from GitHub with:

install.packages("devtools")  # if not already installed
devtools::install_github("WeirauchLab/mpraprofiler")

To build the vignette(s), install some additional packages

install.packages("tidyverse")
install.packages("readxl")

# You'll need Bioconductor to get DESeq2
install.packages("BiocManager")
BiocManager::install('DESeq2')

…and add build_vignettes = TRUE to the install command:

devtools::install_github("WeirauchLab/mpraprofiler", build_vignettes = TRUE,
                         force = TRUE)

Example Usage

Please refer to vignettes/sample_analysis.md for details.

How to cite

Xiaoming Lu, mpraprofiler, (2020), GitHub repository, https://github.com/WeirauchLab/mpraprofiler

Contributors

| Name | Institution | Remarks | |-----------------|--------------------------------|-----------------------------------------| | Dr. Xiaoming Lu | Cincinnati Children’s Hospital | primary author | | Kevin Ernst | Cincinnati Children’s Hospital | minor documentation and packaging fixes |

License

Copyleft Cincinnati Children’s Hospital Medical Center and contributors.

Released under the terms of the GNU General Public License v3. See LICENSE.md for details.

lux2ht/mpraprofiler documentation built on July 4, 2023, 5:45 a.m.