An R package for analyzing covalent labeling-mass spectrometry data coADAPTr is an R package for analyzing covalent labeling-mass spectrometry experimental data that has been sequence searched on a platform like Proteome Discoverer (v2.3+). The package provides functions for quality control, data normalization for quantitation, visualization, and statistical analysis of covalent labeling-mass spectrometry data.
Features Quality Control: Check the quality of your data and remove duplicates.
Visualization: Create informative plots to visualize the data and the results of statistical analysis.
Statistical Analysis: Perform differential analysis, and classification and extent of modification quantification of covalent labeling-mass spectrometry data.
Installation: You can install the package from GitHub using the devtools package copy code:
Replace "username" with the actual username of the repository.
devtools::install_github("username/coADAPTr")
Usage To get started, load the package in R copy code:
library(coADAPTr)
install.packages('rmarkdown', dep = TRUE) name: Using coADAPTr
For more information and a step by step guide on how to use the package, see the vignettes copy code:
vignette("coADAPTr-introduction")
This package was developed by Dr. Raquel L. Shortt of the Dr. Lisa M. Jones Lab at The University of California San Diego alongside Dr. Lindsay Pino of Talus Bioscience. We gratefully acknowledge the support of our funding agencies and the helpful comments of our colleagues.
This package is released under the GNU General Public License v3.0.