FragPipeAnalystR

R package for FragPipe downstream analysis. FragPipeAnalystR is the core of FragPipe-Analyst Shiny App.

Installation

We recommend to use renv for managing your R environment dependencies

renv::install("bioc::ComplexHeatmap")
renv::install("bioc::limma")
renv::install("bioc::MSnbase")
renv::install("bioc::SummarizedExperiment")
renv::install("bioc::cmapR")
renv::install("bioc::ConsensusClusterPlus")
renv::install("Nesvilab/FragPipeAnalystR")

# optional
renv::install("nicolerg/ssGSEA2")

Tutorial

• LFQ AP-MS protein level analysis
• TMT ccRCC protein level analysis

• DIA ccRCC protein level analysis

• TMT ccRCC phosphosite analysis

Reference

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R. Steele, Ralf B. Schittenhelm, Alexey I. Nesvizhskii bioRxiv 2024.03.05.583643; doi: https://doi.org/10.1101/2024.03.05.583643

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