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-any)MSstatsBioNet_1.4.1.zip(r-4.6-any)
MSstatsBioNet_1.4.1.tgz(r-4.6-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✨
DESCRIPTION |NEWS
card.svg |card.png
MSstatsBioNet/json (API)

# 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-1.5.4(bioc 3.24)MSstatsBioNet-1.4.1(bioc 3.23)

immunooncologymassspectrometryproteomicssoftwarequalitycontrolnetworkenrichmentnetwork

6.71 score 2 stars 1 packages 16 scripts 302 downloads 9 exports 105 dependencies

Last updated from:75d54f9c69 (on RELEASE_3_23). Checks:1 ERROR, 5 NOTE, 2 OK, 2 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR174
linux-develNOTE232
source / vignettesOK231
linux-releaseNOTE233
macos-releaseNOTE108
macos-oldrelFAIL80
windows-develNOTE152
windows-releaseNOTE129
windows-oldrelFAIL273
wasm-releaseOK127

Exports:annotateProteinInfoFromIndracytoscapeNetworkcytoscapeNetworkOutputdeleteEdgeFromNetworkexportNetworkToHTMLfilterSubnetworkByContextgetSubnetworkFromIndrapreviewNetworkInBrowserrenderCytoscapeNetwork

Dependencies:askpassbackportsbase64encbitopsbootbslibcachemcaToolscheckmateclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfloatfontawesomefsgenericsggplot2ggrepelgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrisobandISOcodesjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallgrlifecyclelimmalme4magrittrmarrayMASSMatrixMatrixExtramemoisemimeminqamlapiMSstatsMSstatsConvertnlmenloptropensslotelpillarpkgconfigplotlypreprocessCorepromisespurrrr2rR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrentrezRhpcBLASctlrlangrmarkdownrsparseS7sassscalesstatmodstopwordsstringistringrsurvivalsystext2vectibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLxml2yaml

Filtering Subnetworks by Biological Context
Overview | Input Data | Building the Subnetwork | Step 1 — Annotate proteins with INDRA metadata | Step 2 — Retrieve the interaction subnetwork | Filtering by Context: Tag Count | Defining the Query | Filtered nodes | Filtered edges | Evidence with scores | Defining a cutoff | Filtering by Context: Cosine score | Choosing a score Cutoff | Session Info
Rendered fromFilter-By-Context.Rmdusingknitr::rmarkdown

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

PTM Analysis
Installation | Dataset | ID Conversion | Subnetwork Query | Network Visualization | Session info
Rendered fromPTM-Analysis.Rmdusingknitr::rmarkdown

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

Visualization Engine with CytoscapeJS
Rendered fromCytoscape-Visualization.Rmdusingknitr::rmarkdown

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

MSstatsBioNet Introduction
Installation | Purpose of MSstatsBioNet | Dataset | MSstats Convert from Upstream Dataset | MSstats Process and GroupComparison | MSstatsBioNet Analysis | ID Conversion | Subnetwork Query | Visualize Networks | Session info
Rendered fromMSstatsBioNet.Rmdusingknitr::rmarkdown

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