XINA
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see XINA.
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Bioconductor version: 3.11
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("XINA")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | Network, Proteomics, RNASeq, Software, SystemsBiology |
| Version | 1.6.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| 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 | XINA_1.6.0.tar.gz |
| Windows Binary | XINA_1.6.0.zip |
| macOS 10.13 (High Sierra) | XINA_1.6.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |