Code building for workflow package
This repository will be used to build a customized UConn PMF-SCS workflow for Data-Independent Acquisition (DIA) proteomics data. The code will be expanded to include more options for users, and more detailed explanations of the steps in the analysis process.
Installation
You can install the development version of msDiaLogue from GitHub with:
# install.packages("devtools")
devtools::install_github("uconn-scs/msDiaLogue")For Windows, the RTools is required to build this package.
Main areas include
- Data preprocessing: getting data from Spectronaut
- Data transformation: options for transforming abundance data
- Data filtering: providing options to filter out data based on preset levels
- Data normalization: normalization procedures
- Data imputation: missing data procedures
- Data summary: calculating and presenting numerical summaries in tabular form
- Differential Abundance Analysis: statistical tools for DIA data analysis
- Data visualization: providing clean visuals to aid in data analysis decisions