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msDiaLogue

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")

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

General problems during installation

  1. WARNING: Rtools is required to build R packages but is not currently installed.

For Windows, the RTools is required to build this package.

  1. sh: /opt/gfortran/bin/gfortran: No such file or directory

The GFortran compiler is required to build this package.