brandoninvergo / ptxqc Goto Github PK

This package allows users of MaxQuant to generate quality control reports in PDF format.

• plethora of quality metrics
  • intensity distributions
  • digestion efficiency
  • contaminant visualizations
  • identification performance
• easy usage (drag'n'drop your txt output folder onto a batch file)
  • 10 min installation, see ['inst' subfolder] 1
• PDF report will be generated within your txt folder
• optional configuration file in YAML format for generation of shorter/customized reports

• MaxQuant users (no knowledge of R required)
• bioinformaticians (who want to contribute or customize)

If you want to generate QC reports without actually getting involved in R:

See ['inst' subfolder] 1 . It takes 10 minutes and you are done!

If you are a developer and just want the package:

Direct installation from GitHub requires the 'devtools' package. The following lines will add PTXQC on a fresh R installation:

install.packages("devtools")
library("devtools")             ## this might give a warning like 'WARNING: Rtools is required ...'. Ignore it.
source("http://bioconductor.org/biocLite.R")
biocLite("Biobase)
install_github("cbielow/PTXQC") 
help(package="PTXQC")           ## all done; check out the documentation

• Windows (recommended for convenience to make use of the drag'n'drop batch file provided)
• Linux
• MacOSX