protools2

A Set Of Tools For Proteomics And Phosphoproteomics Data Analysis

Reads and normalises proteomic and phosphoproteomic data. Does statistical analysis using limma or t-test. It also incorporates functions for KSEA, pathway analysis and network visualisation tools.

Installation

RStudio

1. Download the Package Archive File (protools2_x.x.x.tar.gz) of the latest release.
   • Not the Source code
2. In RStudio, click: Tools menu
3. Select: Install Packages...
4. In the Install from list box, select: Package Archive File (.zip; .tar.gz)
5. Click: Browse to select the downloaded protools2 Package Archive File
6. Select: Install

R console

One-liner

Run: devtools::install_github("CutillasLab/protools2@*release")

• You may first need to install devtools: install.packages("devtools")

Manual

1. Download the Package Archive File (protools2_x.x.x.tar.gz) of the latest release.
   • Not the Source code
2. Run: devtools::install_local(path = "C:/path/to/protools2_x.x.x.tar.gz")
   • Replace the string argument to path with the actual location
   • You may first need to install devtools: install.packages("devtools")

Errors

If you encounter errors stating that certain required packages are missing, try manually installing the missing packages listed prior to reattempting to install protools2:

• install.packages("package_name")
• Replace "package_name" with each of the packages listed in the R console in turn

Usage

Where possible, use _edit variants of functions as this will execute the latest implementation. The package is in the process of being updated and so original functions are kept with the same name for backwards compatibility.