PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.

@article{Nagaraj2015PGToolsAS,
  title={PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.},
  author={Shivashankar H. Nagaraj and Nicola Waddell and Anil K Madugundu and Scott Wood and Alun Jones and Ramya A. Mandyam and Katia Nones and John V. Pearson and Sean M. Grimmond},
  journal={Journal of proteome research},
  year={2015},
  volume={14 5},
  pages={2255-66}
}
We describe PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools comprises applications, libraries, customized databases, and visualization tools for analysis of mass-spectrometry data using combined proteomic and genomic backgrounds. A single command is sufficient to search databases, calculate false discovery rates, group and annotate proteins, generate peptide databases from RNA-Seq transcripts, identify altered proteins associated with cancer… CONTINUE READING
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