Package: MSstatsBioNet 1.4.1

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_1.4.1.tar.gz
MSstatsBioNet_1.4.1.zip(r-4.7)MSstatsBioNet_1.4.1.zip(r-4.6)MSstatsBioNet_1.4.1.zip(r-4.5)
MSstatsBioNet_1.4.1.tgz(r-4.6-any)MSstatsBioNet_1.4.1.tgz(r-4.5-any)
MSstatsBioNet_1.4.1.tar.gz(r-4.7-any)MSstatsBioNet_1.4.1.tar.gz(r-4.6-any)
MSstatsBioNet_1.4.1.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-release.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

6.71 score 2 stars 1 packages 12 scripts 252 downloads 9 exports 106 dependencies

Last updated from:75d54f9c69 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR245
linux-devel-x86_64NOTE242
source / vignettesOK348
linux-release-x86_64NOTE251
macos-release-arm64NOTE125
macos-oldrel-arm64NOTE129
windows-develNOTE146
windows-releaseNOTE135
windows-oldrelNOTE175
wasm-releaseOK196

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