Workflow Package: proteomics

Mass spectrometry and proteomics data analysis

Bioconductor version: Release (3.8)

This workflow illustrates R / Bioconductor infrastructure for proteomics. Topics covered focus on support for open community-driven formats for raw data and identification results, packages for peptide-spectrum matching, data processing and analysis.

Author: Laurent Gatto [aut, cre]

Maintainer: Laurent Gatto <lg390 at cam.ac.uk>

Citation (from within R, enter citation("proteomics")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("proteomics", version = "3.8")

Documentation

To view available workflows for the version of this package installed in your system, start R and enter:

browseVignettes("proteomics")

 

HTML R Script An R/Bioc proteomics workflow

Details

biocViews ProteomicsWorkflow, Workflow
Version 1.4.0
License Artistic-2.0
Depends R (>= 3.3.0), mzR, mzID, MSnID, MSnbase, rpx, MLInterfaces, pRoloc, pRolocdata, MSGFplus, rols, hpar
Imports
LinkingTo
Suggests knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL https://www.bioconductor.org/help/workflows/proteomics/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

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