Package: chroGPS
Type: Package
Title: chroGPS2: Generation, visualization and differential analysis of
        epigenome maps
Version: 2.4.0
Date: 2019-05-31
Author: Oscar Reina, David Rossell
Maintainer: Oscar Reina <oscar.reina@irbbarcelona.org>
Description: We provide intuitive maps to visualize, analyze and compare the association between genetic elements based on their epigenetic profiles. The approach is based on Multi-Dimensional Scaling, and includes a parallelized implementation for handling high dimensional datasets. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds. We also provide functions and methods to perform differential analysis of epigenome maps at factor and gene level.
License: GPL (>=2.14)
Depends: R (>= 3.2.0), GenomicRanges, IRanges, methods, Biobase, MASS,
        graphics, stats, changepoint
#Imports: graphics, cluster, DPpackage, ICSNP
Imports: cluster, DPpackage, ICSNP, ellipse, vegan
Enhances: parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno,
        org.Dm.eg.db, caTools, plotly
Collate: adjustPeaks.R distGPS.R domainDist.R mds-class.R mds.R
        procrustesAdj.R clusGPS.R geneSetGPS.R getmodEncode.R
        gff2RDList.R gps2xgmml.R diffFactors.R diffGenes.R
        mergeReplicates.R profileClusters.R rankFactorsbyDomain.R
        rankFactorsbyProfile.R
LazyLoad: yes
biocViews: Epigenetics, Clustering, ChIPchip, ChIPSeq,
        HistoneModification, Visualization, DataRepresentation,
        ImmunoOncology
git_url: https://git.bioconductor.org/packages/chroGPS
git_branch: RELEASE_3_10
git_last_commit: 3f20425
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: no
Packaged: 2019-10-30 02:15:22 UTC; biocbuild
Built: R 3.6.1; ; 2019-10-30 12:54:07 UTC; windows
