Package: MSstatsBioNet 1.5.5

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_1.5.5.tar.gz
MSstatsBioNet_1.5.5.zip(r-4.7-any)MSstatsBioNet_1.5.5.zip(r-4.6-any)MSstatsBioNet_1.5.5.zip(r-4.5-any)
MSstatsBioNet_1.5.5.tgz(r-4.6-any)MSstatsBioNet_1.5.5.tgz(r-4.5-any)
MSstatsBioNet_1.5.5.tar.gz(r-4.7-any)MSstatsBioNet_1.5.5.tar.gz(r-4.6-any)
MSstatsBioNet_1.5.5.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.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

7.08 score 2 stars 1 packages 15 scripts 302 downloads 32 exports 105 dependencies

Last updated from:a9e97749a7. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR178
linux-develNOTE375
source / vignettesOK472
linux-releaseNOTE238
macos-releaseNOTE172
macos-oldrelNOTE143
windows-develNOTE180
windows-releaseNOTE179
windows-oldrelNOTE175
wasm-releaseOK132

Exports:add_entity_valuesannotateProteinInfoFromIndrabackend_capabilitiesbootstrapTopicModelscompareTopicModelsconvert_idscytoscapeNetworkcytoscapeNetworkOutputdecomposeSubnetworkByTopicdecomposeSubnetworkIntoHierarchicalTopicsdeleteEdgeFromNetworkexportNetworkToHTMLfilter_by_curationfilter_by_ptm_sitefilterSubnetworkByContextget_curationsget_entity_propertiesget_evidenceget_networkgetSubnetworkFromIndraindra_backendINDRA_DATABASE_SOURCESINDRA_TEXT_MINED_SOURCESload_networkmerge_networksprepare_entitiespreviewNetworkInBrowserrenderCytoscapeNetworksave_networkselect_entitiessubnetwork_queryvalidate_network

Dependencies:askpassbackportsbase64encbitopsbootbslibcachemcaToolscheckmateclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfloatfontawesomefsgenericsggplot2ggrepelgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttrisobandISOcodesjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallgrlifecyclelimmalme4magrittrmarrayMASSMatrixMatrixExtramemoisemimeminqamlapiMSstatsMSstatsConvertnlmenloptropensslotelpillarpkgconfigplotlypreprocessCorepromisespurrrr2rR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrentrezRhpcBLASctlrlangrmarkdownrsparseS7sassscalesstatmodstopwordsstringistringrsurvivalsystext2vectibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLxml2yaml

PTM Analysis with Global Profiling
Installation | Purpose of this vignette | Dataset | Building the entity tables | ID Conversion | Selecting Sites | Network Query | Sites only | Adding kinases with include_entities | Adding global profiling values | Reading the network | Network Visualization | Session info
Rendered fromPTM-Analysis.Rmdusingknitr::rmarkdown

Last update: 2026-10-14
Started: 2025-09-11

Metabolomics Analysis
Installation | Purpose of this vignette | Dataset | Building the entity table | ID Conversion | Selecting Compounds | Network Query | Measured compounds only | Adding proteins with include_entities | Compounds detected at one time point only | Network Visualization | Session info
Rendered fromMetabolomics-Analysis.Rmdusingknitr::rmarkdown

Last update: 2026-10-07
Started: 2026-10-07

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

Last update: 2026-10-06
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: 2026-10-05
Started: 2024-07-25

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 | Excluding abstracts by keyword | Decomposing the filtered network into topics | Session Info
Rendered fromFilter-By-Context.Rmdusingknitr::rmarkdown

Last update: 2026-10-05
Started: 2026-03-11

Readme and manuals

Help Manual

Help pageTopics
Validate Annotate Protein Info Input.validateAnnotateProteinInfoFromIndraInput
Copy the values of an entity table onto a network's nodesadd_entity_values
Annotate Protein Information from IndraannotateProteinInfoFromIndra
What a backend supportsbackend_capabilities backend_capabilities,IndraBackend-method backend_capabilities,NetworkBackend-method
Bootstrap the topic decomposition to find each topic's robust top wordsbootstrapTopicModels
Test whether including PPIs changes topic structure beyond random chancecompareTopicModels
Ground entities in a backend's namespacesconvert_ids convert_ids,IndraBackend-method convert_ids,NetworkBackend-method
Render a Cytoscape network visualisationcytoscapeNetwork
Shiny output binding for cytoscapeNetworkcytoscapeNetworkOutput
Decompose a subnetwork into topic-specific subnetworks via joint NMFdecomposeSubnetworkByTopic
Recursively decompose a subnetwork into a hierarchy of topic subnetworksdecomposeSubnetworkIntoHierarchicalTopics
Delete an edge from a network edges data framedeleteEdgeFromNetwork
Export network data with Cytoscape visualizationexportNetworkToHTML
Remove evidence curated as incorrectfilter_by_curation
Keep the edges that modify a PTM site in the networkfilter_by_ptm_site
Filter a subnetwork by contextual relevancefilterSubnetworkByContext
Get the curations of edges from a backendget_curations get_curations,IndraBackend-method get_curations,NetworkBackend-method
Add a backend's properties of each entityget_entity_properties get_entity_properties,IndraBackend-method get_entity_properties,NetworkBackend-method
Get the evidence behind network edgesget_evidence get_evidence,IndraBackend-method get_evidence,NetworkBackend-method
Get a network from a backendget_network get_network,IndraBackend,SubnetworkQuery-method get_network,NetworkBackend,missing-method get_network,NetworkBackend,NetworkQuery-method
Get subnetwork from INDRA databasegetSubnetworkFromIndra
Create an INDRA backendindra_backend
Evidence sources of INDRAINDRA_DATABASE_SOURCES indra_evidence_sources INDRA_TEXT_MINED_SOURCES
Load a network saved with save_network()load_network
Combine networks from several queries or backendsmerge_networks
Questions you can ask of a network backendnetwork_queries
Network backend classesIndraBackend-class NetworkBackend-class
Network query classesNetworkQuery-class SubnetworkQuery-class
Prepare an entity table from MSstats resultsprepare_entities
Preview network in browserpreviewNetworkInBrowser
Print a topic hierarchy as an indented treeprint.topicHierarchy
Render a Cytoscape network in a Shiny application. This function is used to render a Cytoscape network visualization within a Shiny application.renderCytoscapeNetwork
Save a network to a filesave_network
Flag the entities to queryselect_entities
How are my selected entities connected to each other?subnetwork_query
Validate a network against the edge and node contractvalidate_network