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")

Get started

To use FragPipeAnalystR, follow the same instruction for preparing the input file for FragPipe-Analyst.

Tutorial

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

• DIA ccRCC protein level analysis

• TMT ccRCC phosphosite analysis

Reference

Yi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R. Steele, Ralf B. Schittenhelm, and Alexey I. Nesvizhskii Journal of Proteome Research (2024), DOI: 10.1021/acs.jproteome.4c00294

This site is open source. Improve this page.