Package: XINA
Type: Package
Title: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network
        Analysis
Version: 1.29.0
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: devel
git_last_commit: 6e730aa
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-11-12
NeedsCompilation: no
Packaged: 2025-11-12 22:29:18 UTC; biocbuild
Built: R 4.6.0; ; 2025-11-13 02:14:03 UTC; unix
