Package: XINA
Type: Package
Title: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network
        Analysis
Version: 1.28.0
biocViews: SystemsBiology, Proteomics, RNASeq, Network
Author: Lang Ho Lee <lhlee@bwh.harvard.edu> and Sasha A. Singh
        <sasingh@bwh.harvard.edu>
Maintainer: Lang Ho Lee <lhlee@bwh.harvard.edu> and Sasha A. Singh
 <sasingh@bwh.harvard.edu>
Authors@R: c(person("Lang Ho", "Lee", email="lhlee@bwh.harvard.edu",  
	      role = c("aut", "cre")), 
	      person("Sasha", "Singh", email="sasingh@bwh.harvard.edu", 
	      role = c("aut")))
Description: 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.
Copyright: XINA combines multiple quantitative (kinetics) datasets from
        omics studies into a single input dataset for clustering.
        Copyright(C)2018 Lang Ho Lee, Arda Halu, Stephanie Morgan,
        Hiroshi Iwata, Masanori Aikawa, and Sasha A. Singh This program
        is free software: you can redistribute it and/or modify it
        under the terms of the GNU General Public License as published
        by the Free Software Foundation, either version 3 of the
        License, any later version. This program is distributed in the
        hope that it will be useful, but WITHOUT ANY WARRANTY; without
        even the implied warranty of MERCHANTABILITY or FITNESS FOR A
        PARTICULAR PURPOSE. See the GNU General Public License for more
        details. You should have received a copy of the GNU General
        Public License along with this program. If not, see
        <https://www.gnu.org/licenses/>. - Contact emails: L. Lee,
        LHLEE@BWH.HARVARD.EDU S. Singh, SASINGH@BWH.HARVARD.EDU M.
        Aikawa, MAIKAWA@BWH.HARVARD.EDU - Mailing address: Department
        of Medicine, Cardiovascular Division Center for Interdisciplin
        ary Cardiovascular Sciences 3 Blackfan Street, 17th Floor
        Boston, MA 02115 USA
License: GPL-3
Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
        grDevices, graphics, utils, STRINGdb
VignetteBuilder: knitr
LazyData: FALSE
RoxygenNote: 6.1.1
Encoding: UTF-8
Depends: R (>= 3.5)
Suggests: knitr, rmarkdown
Date: 2019-01-31
git_url: https://git.bioconductor.org/packages/xina
git_branch: master
git_last_commit: 897b60b
Config/pak/sysreqs: libglpk-dev libpng-dev libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:47:19 UTC
RemoteUrl: https://github.com/bioc/XINA
RemoteRef: RELEASE_3_22
RemoteSha: a4cb97bd75532b12badee24e8e6d611f29e719fc
NeedsCompilation: no
Packaged: 2025-11-11 18:34:15 UTC; root
Built: R 4.5.2; ; 2025-11-11 18:35:50 UTC; windows
