XINA

DOI: 10.18129/B9.bioc.XINA    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see XINA.

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	xina_user_code
PDF		Reference Manual
Text		NEWS

Details

biocViews	Network, Proteomics, RNASeq, Software, SystemsBiology
Version	1.8.0
In Bioconductor since	BioC 3.8 (R-3.5) (2.5 years)
License	GPL-3
Depends	R (>= 3.5)
Imports	mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	XINA_1.8.0.tar.gz
Windows Binary	XINA_1.8.0.zip
macOS 10.13 (High Sierra)	XINA_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/XINA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/XINA
Package Short Url	https://bioconductor.org/packages/XINA/
Package Downloads Report	Download Stats