Package: MSstatsBioNet 0.99.9
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:
MSstatsBioNet_0.99.9.tar.gz
MSstatsBioNet_0.99.9.zip(r-4.5)MSstatsBioNet_0.99.9.zip(r-4.4)
MSstatsBioNet_0.99.9.tgz(r-4.5-any)MSstatsBioNet_0.99.9.tgz(r-4.4-any)
MSstatsBioNet_0.99.9.tar.gz(r-4.5-noble)MSstatsBioNet_0.99.9.tar.gz(r-4.4-noble)
MSstatsBioNet_0.99.9.tgz(r-4.4-emscripten)
MSstatsBioNet.pdf |MSstatsBioNet.html✨
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 site:https://vitek-lab.github.io
On BioConductor:MSstatsBioNet-0.99.9(bioc 3.21)
immunooncologymassspectrometryproteomicssoftwarequalitycontrolnetworkenrichmentnetwork
Last updated 15 days agofrom:3dbd25254d. Checks:1 OK, 5 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 22 2025 |
| R-4.5-win | NOTE | Feb 22 2025 |
| R-4.5-mac | NOTE | Feb 22 2025 |
| R-4.5-linux | NOTE | Feb 22 2025 |
| R-4.4-win | NOTE | Feb 22 2025 |
| R-4.4-mac | NOTE | Feb 22 2025 |
Exports:annotateProteinInfoFromIndragetSubnetworkFromIndravisualizeNetworks
Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopsbootbslibcachemcaToolscheckmateclicolorspacecpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2ggrepelgluegplotsgraphgtablegtoolshighrhtmltoolshtmlwidgetshttrIRdisplayIRkernelisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmalme4log4rmagrittrmarrayMASSMatrixmemoisemgcvmimeminqaMSstatsMSstatsConvertmunsellnlmenloptropensslpbdZMQpillarpkgconfigplotlypreprocessCorepromisespurrrr2rR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRCy3RdpackreformulasreprRJSONIOrlangrmarkdownsassscalesstatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexutf8uuidvctrsviridisLitewithrxfunXMLyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Populate HGNC IDs in Data Frame | .populateHgncIdsInDataFrame |
| Populate HGNC Names in Data Frame | .populateHgncNamesInDataFrame |
| Populate Kinase Info in Data Frame | .populateKinaseInfoInDataFrame |
| Populate Phosphatase Info in Data Frame | .populatePhophataseInfoInDataFrame |
| Populate Transcription Factor Info in Data Frame | .populateTranscriptionFactorInfoInDataFrame |
| Populate Uniprot IDs in Data Frame | .populateUniprotIdsInDataFrame |
| Validate Annotate Protein Info Input | .validateAnnotateProteinInfoFromIndraInput |
| Annotate Protein Information from Indra | annotateProteinInfoFromIndra |
| Get subnetwork from INDRA database | getSubnetworkFromIndra |
| Create visualization of network | visualizeNetworks |
