The goal of mpraprofiler is to create a simple tool to perform allelic differential expression analysis for massively parallel reporter assay (MPRA) data.
You can install mpraprofiler from GitHub with:
install.packages("devtools") # if not already installed
devtools::install_github("WeirauchLab/mpraprofiler")You'll also need the following packages, if not already available:
install.packages("tidyverse")
install.packages("readxl")
install.packages("BiocManager")
BiocManager::install('DESeq2')
# only required if you're building the vignettes
install.packages("formatR")To build the vignette(s), add build_vignettes = TRUE to the install command:
devtools::install_github("WeirauchLab/mpraprofiler", build_vignettes = TRUE,
force = TRUE)Clone the repository locally:
cd wherever/you/keep/source/code
git clone https://github.com/WeirauchLab/mpraprofiler.git
cd mpraprofilerInstall the third-party packages mentioned above, then, in an interactive R session, install mpraprofiler:
install.packages(getwd(), repos = NULL, source = TRUE)
# or, if you have 'devtools' installed
devtools::install(build_vignettes = TRUE)You can also build local copies of the vignettes using the make vignettes
target of the included Makefile.
Please refer to vignettes/sample_analysis.md
for details.
Lu, X. (2020). WeirauchLab/mpraprofiler. Zenodo. https://doi.org/10.5281/zenodo.20932500
This DOI will always redirect to the latest version. The corresponding publication may be cited as:
Lu, X., Chen, X., Forney, C. et al. Global discovery of lupus genetic risk variant allelic enhancer activity. Nat Commun 12, 1611 (2021). https://doi.org/10.1038/s41467-021-21854-5
| Name | Institution | Remarks |
|---|---|---|
| Dr. Xiaoming Lu | Cincinnati Children's Hospital | primary author |
| Kevin Ernst | Cincinnati Children's Hospital | minor documentation and packaging fixes |
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.