https://github.com/merck/rcpdms
Chemoproteomics Data Analysis
https://github.com/merck/rcpdms
Last synced: 9 months ago
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Chemoproteomics Data Analysis
- Host: GitHub
- URL: https://github.com/merck/rcpdms
- Owner: Merck
- License: gpl-3.0
- Created: 2019-07-08T17:18:04.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-07-08T17:30:01.000Z (almost 7 years ago)
- Last Synced: 2025-03-18T01:36:00.607Z (about 1 year ago)
- Language: R
- Size: 254 KB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Chemoproteomics Data Analysis
========================================
Authors: Yuting Xu, Andy Liaw, Huijun Wang
Copyright© 2019 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA.
Last updated: 07/03/2019
Requirements
----------------
* R (>= 3.4.0)
* R packages: drc, truncnorm, magrittr, dplyr, knitr, ggplot2, gridExtra, reshape2, tidyr, limma
Install
----------------
- Option 1) Install from github
``` r
if('rCPDMS' %in% installed.packages()){remove.packages('rCPDMS')}
# install.packages("devtools")
devtools::install_github("Merck/rCPDMS")
```
- Option 2) Install from R-package source file rCPDMS_0.1.3.tar.gz in this repository
``` r
if('rCPDMS' %in% installed.packages()){remove.packages('rCPDMS')}
install.packages("rCPDMS_0.1.3.tar.gz", repos = NULL, type = "source")
```
Usage
----------------
Follow the scripts in demo/demo_CPDMS.R to set parameters for model fitting.
Example datasets are included in folder data_raw.
Workflows
----------------
* Pull down
* Cellular Thermal Shift Assay (CETSA)
* Iso-Thermal Dose Response (2dCETSA)
Notes
----------------
The example code in miscellaneous/processMaxquantProtein.R demonstrates how to take a maxquant protein output (protein.txt) and the mapping file (MappingTemplaete.csv) to generate input data file for rCPDMS package.