Package: MSstatsBioNet 1.5.1

Anthony Wu

MSstatsBioNet: Network Analysis for MS-based Proteomics Experiments

A set of tools for network analysis using mass spectrometry-based proteomics data and network databases. The package takes as input the output of MSstats differential abundance analysis and provides functions to perform enrichment analysis and visualization in the context of prior knowledge from past literature. Notably, this package integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques.

Authors:Anthony Wu [aut, cre], Olga Vitek [aut]

MSstatsBioNet_1.5.1.tar.gz
MSstatsBioNet_1.5.1.zip(r-4.7)MSstatsBioNet_1.5.1.zip(r-4.6)MSstatsBioNet_1.5.1.zip(r-4.5)
MSstatsBioNet_1.5.1.tgz(r-4.6-any)MSstatsBioNet_1.5.1.tgz(r-4.5-any)
MSstatsBioNet_1.5.1.tar.gz(r-4.7-any)MSstatsBioNet_1.5.1.tar.gz(r-4.6-any)
MSstatsBioNet_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MSstatsBioNet/json (API)
NEWS

# Install 'MSstatsBioNet' in R:
install.packages('MSstatsBioNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vitek-lab/msstatsbionet/issues

Pkgdown/docs site:https://vitek-lab.github.io

On BioConductor:MSstatsBioNet-1.5.1(bioc 3.24)MSstatsBioNet-1.4.1(bioc 3.23)

immunooncologymassspectrometryproteomicssoftwarequalitycontrolnetworkenrichmentnetwork

6.77 score 2 stars 1 packages 13 scripts 252 downloads 9 exports 106 dependencies

Last updated from:d1e62195f8. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR195
linux-devel-x86_64NOTE240
source / vignettesOK272
linux-release-x86_64NOTE240
macos-release-arm64NOTE109
macos-oldrel-arm64NOTE160
windows-develNOTE147
windows-releaseNOTE127
windows-oldrelNOTE148
wasm-releaseOK137

Exports:annotateProteinInfoFromIndracytoscapeNetworkcytoscapeNetworkOutputdeleteEdgeFromNetworkexportNetworkToHTMLfilterSubnetworkByContextgetSubnetworkFromIndrapreviewNetworkInBrowserrenderCytoscapeNetwork

Dependencies:askpassbackportsbase64encbitopsbootbslibcachemcaToolscheckmateclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfloatfontawesomefsgenericsggplot2ggrepelgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrisobandISOcodesjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallgrlifecyclelimmalme4log4rmagrittrmarrayMASSMatrixMatrixExtramemoisemimeminqamlapiMSstatsMSstatsConvertnlmenloptropensslotelpillarpkgconfigplotlypreprocessCorepromisespurrrr2rR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrentrezRhpcBLASctlrlangrmarkdownrsparseS7sassscalesstatmodstopwordsstringistringrsurvivalsystext2vectibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLxml2yaml

Filtering Subnetworks by Biological Context

Rendered fromFilter-By-Context.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-03-11
Started: 2026-03-11

MSstatsBioNet Introduction

Anthony Wu

Rendered fromMSstatsBioNet.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-09-11
Started: 2024-07-25

PTM Analysis

Anthony Wu

Rendered fromPTM-Analysis.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-03-01
Started: 2025-09-11

Visualization Engine with CytoscapeJS

Anthony Wu

Rendered fromCytoscape-Visualization.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-03-01
Started: 2026-02-27