XINA

DOI: 10.18129/B9.bioc.XINA    

This is the development version of XINA; for the stable release version, see XINA.

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Bioconductor version: Development (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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.7.0
In Bioconductor since BioC 3.8 (R-3.5) (2 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_1.7.0.tar.gz
Windows Binary XINA_1.7.0.zip
macOS 10.13 (High Sierra) XINA_1.7.0.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

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