diff --git a/DESCRIPTION b/DESCRIPTION index cc1f221..5eac804 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,18 +1,18 @@ Package: MSstatsBioNet Type: Package -Title: Protein-Protein Interaction Analysis for MS-based Proteomics Experiments -Version: 0.1.0 +Title: Network Analysis for MS-based Proteomics Experiments +Version: 0.99.0 Authors@R: c( person("Anthony", "Wu", email = "wu.anthon@northeastern.edu", role = c("aut", "cre")), person("Olga", "Vitek", email = "o.vitek@northeastern.edu", role = "aut", comment=c(ORCID = "0000-0003-1728-1104"))) -Description: A set of tools for protein-protein interaction analysis using mass +Description: 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 protein-protein interactions + integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques. License: Artistic-2.0 Depends: R (>= 4.4.0) @@ -30,7 +30,7 @@ Suggests: mockery VignetteBuilder: knitr biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, - QualityControl + QualityControl, NetworkEnrichment, Network Encoding: UTF-8 URL: http://msstats.org, https://vitek-lab.github.io/MSstatsBioNet/ BugReports: https://groups.google.com/forum/#!forum/msstats diff --git a/NEWS.md b/NEWS.md index e3c9a3a..259a885 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# MSstatsBioNet 0.99.0 + +* Added function `getSubnetworkFromIndra` to extract biomolecular subnetworks +from the INDRA database. +* Added function `visualizeNetworks` to visualize networks in Cytoscape desktop. +* Added vignette + # MSstatsBioNet 0.1.0 * Added a `NEWS.md` file to track changes to the package. \ No newline at end of file diff --git a/R/visualizeNetworks.R b/R/visualizeNetworks.R index ddad431..6ec8520 100644 --- a/R/visualizeNetworks.R +++ b/R/visualizeNetworks.R @@ -23,7 +23,7 @@ #' #' visualizeNetworks <- function(nodes, edges, - pvalue_cutoff = 0.05, logfc_cutoff = 0.5) { + pvalue_cutoff = 0.05, logfc_cutoff = 0.5) { # Add additional columns for visualization nodes$logFC_color <- nodes$logFC nodes$logFC_color[nodes$pvalue > pvalue_cutoff | diff --git a/README.md b/README.md index 7a7b5aa..0956829 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,22 @@ This package provides a suite of functions to query various network databases, filter queries & results, and visualize networks. +## Installation Instructions + +To install this package on bioconductor, run the following command: +``` +if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("MSstatsBioNet") +``` + +You can install the development version of this package through Github: + +``` +devtools::install_github("Vitek-Lab/MSstatsConvert", build_vignettes = TRUE) +``` + ## Databases Supported - INDRA diff --git a/vignettes/MSstatsBioNet.Rmd b/vignettes/MSstatsBioNet.Rmd index b4c9d40..e8a0197 100644 --- a/vignettes/MSstatsBioNet.Rmd +++ b/vignettes/MSstatsBioNet.Rmd @@ -19,7 +19,7 @@ library(MSstatsBioNet) ``` # Purpose of MSstatsBioNet - + The `MSstatsBioNet` package is a member of the `MSstats` family of packages. It contains a set of functions for interpretation of mass spectrometry (MS) statistical analysis results in the context of protein-protein interaction @@ -40,3 +40,10 @@ input <- data.table::fread( subnetwork <- getSubnetworkFromIndra(input) visualizeNetworks(subnetwork$nodes, subnetwork$edges) ``` + + +# Session info + +```{r} +sessionInfo() +``` \ No newline at end of file