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XINA

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis


Bioconductor version: Release (3.18)

The aim of XINA is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. XINA imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. XINA, not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs.

Author: Lang Ho Lee <lhlee at bwh.harvard.edu> and Sasha A. Singh <sasingh at bwh.harvard.edu>

Maintainer: Lang Ho Lee <lhlee at bwh.harvard.edu> and Sasha A. Singh <sasingh at bwh.harvard.edu>

Citation (from within R, enter citation("XINA")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("XINA")

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("XINA")
xina_user_code HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Network, Proteomics, RNASeq, Software, SystemsBiology
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3
Depends R (>= 3.5)
Imports mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb
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Suggests knitr, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package XINA_1.20.0.tar.gz
Windows Binary XINA_1.20.0.zip
macOS Binary (x86_64) XINA_1.20.0.tgz
macOS Binary (arm64) XINA_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/XINA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/XINA
Bioc Package Browser https://code.bioconductor.org/browse/XINA/
Package Short Url https://bioconductor.org/packages/XINA/
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