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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| xina_user_code | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Network, Proteomics, RNASeq, Software, SystemsBiology |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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_1.31.0.tar.gz |
| Windows Binary (x86_64) | XINA_1.31.0.zip |
| macOS Binary (big-sur-x86_64) | XINA_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | XINA_1.31.0.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 |