search

wenbostar / proteoQC

proteoQC: an R package for proteomics data quality assessment.
http://bioconductor.org/packages/devel/bioc/html/proteoQC.html
5 stars 5 forks source link
bioconductor bioinformatics mass-spectrometry mass-spectromtry msms proteomics quality-control r visualization

readme

Build Status Bioconductor release build Status Bioconductor devel build Status

proteoQC

proteoQC is an R package for proteomics data quality assessment. This package creates an HTML format QC report for MS/MS-based proteomics data. The report is intended to allow the user to quickly assess the quality of proteomics data. The official page is the Bioconductor landing page (release or devel versions).

Installation

To install proteoQC

library("BiocInstaller")
biocLite("proteoQC")

If you need the github version (not recommended unless you know what you are doing)

biocLite("wenbostar/proteoQC")

Citation

To cite the proteoQC package in publications, please use:

Wen B and Gatto L (2017). proteoQC: An R package for proteomics data quality control. R package version 1.15.0, https://github.com/wenbostar/proteoQC.

List of citations

proteoQC has been cited in the following manuscripts:

  1. Gatto, Laurent, et al. "Visualization of proteomics data using R and Bioconductor." Proteomics 15.8 (2015): 1375-1389.
  2. Bittremieux, Wout, et al. "Computational quality control tools for mass spectrometry proteomics." Proteomics 17.3-4 (2017).
  3. Samandi, Sondos, et al. "Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins." eLife 6 (2017): e27860.
  4. Belghit I, Lock E J, Fumière O, et al. Species-Specific Discrimination of Insect Meals for Aquafeeds by Direct Comparison of Tandem Mass Spectra. Animals, 2019, 9(5): 222.
  5. Walzer M., Vizcaíno J.A. (2020) Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics. In: Matthiesen R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY

Contribution

Contributions to the package are more than welcome.