MSstatsBioNet
This is the development version of MSstatsBioNet; to use it, please install the devel version of Bioconductor.
Network Analysis for MS-based Proteomics Experiments
Bioconductor version: Development (3.21)
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.
Author: Anthony Wu [aut, cre], Olga Vitek [aut] (ORCID:
Maintainer: Anthony Wu <wu.anthon at northeastern.edu>
citation("MSstatsBioNet")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MSstatsBioNet")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MSstatsBioNet")| MSstatsBioNet: Introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Network, NetworkEnrichment, Proteomics, QualityControl, Software |
| Version | 0.99.9 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | file LICENSE |
| Depends | R (>= 4.4.0), MSstats |
| Imports | RCy3, httr, jsonlite, r2r, tidyr |
| System Requirements | |
| URL | http://msstats.org https://vitek-lab.github.io/MSstatsBioNet/ |
| Bug Reports | https://groups.google.com/forum/#!forum/msstats |
See More
| Suggests | data.table, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery, MSstatsConvert |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstatsBioNet_0.99.9.tar.gz |
| Windows Binary (x86_64) | MSstatsBioNet_0.99.9.zip |
| macOS Binary (x86_64) | MSstatsBioNet_0.99.9.tgz |
| macOS Binary (arm64) | MSstatsBioNet_0.99.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSstatsBioNet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSstatsBioNet |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstatsBioNet/ |
| Package Short Url | https://bioconductor.org/packages/MSstatsBioNet/ |
| Package Downloads Report | Download Stats |