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Material for R/Bioconductor Proteomics Workshop at Stellenbosch University, October 2016

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2016-10-rbioc-prot-stellenbosch's Introduction

Material for R/Bioconductor Proteomics Workshop at Stellenbosch University, October 2016

Short URL to this page: http://bit.ly/2016-rbiocprot-sun

Material

Schedule

time Tue.25.Oct Wed.26.Oct Thu.27.Oct
9:00 - 10:00 R/RStudio intro (LG) Identification 1: DB Search and other methods (DT) Advanced quant: Technology selection, Power, Biofluids (DT)
10:00 - 11:00 R (LG) Practical (DT) Bridget Calder, UCT, demos Skyline
11:00 - 11:30 Coffee Coffee Coffee
11:30 - 12:30 R/Bioconductor for proteomics (LG) Identification 2: protein inference and controlling FDR (DT) Missing values (lecture + demo/practical) (LG)
12:30 - 13:30 Lunch Lunch Lunch
13:30 - 14:30 MS data: pwiz and quameter (DT) R/Bioconductor: mzR, mzID, MSnID (LG) Differential expression (t-test for continuous data, count data, limma) (LG)
14:30 - 15:30 Data visualisation (LG) Intro: quantitative proteomics (DT) Multiple testing (LG)
15:30 - 16:00 Coffee Coffee Coffee
16:00 - 17:00 Practical with R: the mzR and MSnbase packages for raw data (LG) The MSnbase package: MSnSets for quantitative proteomics (LG) Wrap-up

LG: Laurent Gatto - DT: David Tabb

Related material and references

  • Teaching material

  • Gatto L. and Christoforou A. Using R and Bioconductor for proteomics data analysis, Biochim Biophys Acta - Proteins and Proteomics, 2013. PMID:23692960 (preprint)

  • Gatto L, Breckels LM, Naake T, Gibb S. Visualisation of proteomics data using R and Bioconductor. Proteomics. 2015 Feb 18. doi: 10.1002/pmic.201400392. PMID:25690415.

  • Gatto L. and Lilley K.S. MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualisation, processing and quantitation, Bioinformatics, 28(2), 288-289, 2012 PMID:22113085

License

The content of this repository is made available under the Creative Commons Attribution license. The following is a human-readable summary of (and not a substitute for) the full legal text of the CC BY 4.0.

You are free:

  • to Share - copy and redistribute the material in any medium or format
  • to Adapt - remix, transform, and build upon the material

for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow these license terms.

Under the following terms:

Attribution - You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.

No additional restrictions - You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

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