chroGPS: chroGPS: visualizing the epigenome

We provide intuitive maps to visualize the association between genetic elements, with emphasis on epigenetics. The approach is based on Multi-Dimensional Scaling. 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.

AuthorOscar Reina, David Rossell
Date of publicationNone
MaintainerOscar Reina <oscar.reina@irbbarcelona.org>
LicenseGPL (>=2.14)
Version1.22.0

View on Bioconductor

Functions

addVar Man page
adjustPeaks Man page
adjustPeaks,GRangesList-method Man page
adjustPeaks-methods Man page
as.matrix,distGPS-method Man page
boostMDS Man page
clusGPS Man page
clusGPS-class Man page
clusGPS,distGPS,mds-method Man page
clusGPS-method Man page
clusGPS-methods Man page
clusNames Man page
clusNames,clusGPS-method Man page
clusterID Man page
clusterID,clusGPS-method Man page
contour2dDP Man page
d Man page
d2 Man page
d3 Man page
distGPS Man page
distGPS-class Man page
distGPS,data.frame-method Man page
distGPS,GRangesList-method Man page
distGPS,matrix-method Man page
distGPS-methods Man page
domainDist Man page
geneSetGPS Man page
geneSetGPS,data.frame,mds,character-method Man page
geneSetGPS,matrix,mds,character-method Man page
geneSetGPS-methods Man page
getPoints Man page
getPoints,mds-method Man page
getR2 Man page
getR2,mds-method Man page
getStress Man page
getStress,mds-method Man page
getURL Man page
gff2RDList Man page
gps2xgmml Man page
gps2xgmml,mds,ANY-method Man page
gps2xgmml,mds-method Man page
hclust-class Man page
is.adj Man page
is.adj,mds-method Man page
mds Man page
mds-class Man page
mds,distGPS,mds-method Man page
mds,distGPS,missing-method Man page
mds-methods Man page
mds,splitDistGPS,missing-method Man page
mergeClusters Man page
mergeClusters,clusGPS-method Man page
mergeClusters,list-method Man page
mergeClusters-methods Man page
plot,clusGPS,ANY-method Man page
plot,clusGPS-method Man page
plotContour Man page
plot,mds,ANY-method Man page
plot,mds-method Man page
procrustesAdj Man page
procrustesAdj,mds,distGPS-method Man page
procrustesAdj-methods Man page
profileClusters Man page
s2 Man page
s2names Man page
s2Seq Man page
s2SeqNames Man page
s2.tab Man page
s2.wt Man page
show,clusGPS-method Man page
show,distGPS-method Man page
show,mds-method Man page
show,splitDistGPS-method Man page
splidDistGPS-class Man page
splitDistGPS-class Man page
splitDistGPS,data.frame-method Man page
splitDistGPS,distGPS-method Man page
splitDistGPS,matrix-method Man page
tabClusters Man page
tabClusters,clusGPS-method Man page
toydists Man page
uniqueCount Man page

Files

chroGPS/DESCRIPTION
chroGPS/NAMESPACE
chroGPS/R
chroGPS/R/adjustPeaks.R chroGPS/R/clusGPS.R chroGPS/R/distGPS.R chroGPS/R/domainDist.R chroGPS/R/geneSetGPS.R chroGPS/R/getmodEncode.R chroGPS/R/gff2RDList.R chroGPS/R/gps2xgmml.R chroGPS/R/mds-class.R chroGPS/R/mds.R chroGPS/R/procrustesAdj.R
chroGPS/build
chroGPS/build/vignette.rds
chroGPS/data
chroGPS/data/datalist
chroGPS/data/s2.RData
chroGPS/data/s2Seq.RData
chroGPS/data/toydists.RData
chroGPS/inst
chroGPS/inst/NEWS
chroGPS/inst/doc
chroGPS/inst/doc/chroGPS.R
chroGPS/inst/doc/chroGPS.Rnw
chroGPS/inst/doc/chroGPS.pdf
chroGPS/man
chroGPS/man/addVar.Rd chroGPS/man/adjustPeaks.Rd chroGPS/man/boostMDS.Rd chroGPS/man/clusGPS-class.Rd chroGPS/man/clusGPS.Rd chroGPS/man/distGPS-class.Rd chroGPS/man/distGPS.Rd chroGPS/man/domainDist.Rd chroGPS/man/geneSetGPS.Rd chroGPS/man/getURL.Rd chroGPS/man/gff2RDList.Rd chroGPS/man/gps2xgmml.Rd chroGPS/man/mds-class.Rd chroGPS/man/mds.Rd chroGPS/man/mergeClusters.Rd chroGPS/man/procrustesAdj.Rd chroGPS/man/profileClusters.Rd chroGPS/man/s2.Rd chroGPS/man/splitDistGPS-class.Rd
chroGPS/vignettes
chroGPS/vignettes/chroGPS-cyto.png
chroGPS/vignettes/chroGPS-cyto3d.png
chroGPS/vignettes/chroGPS.Rnw
chroGPS/vignettes/mds-2d-3d.png
chroGPS/vignettes/mds3d_1.png
chroGPS/vignettes/references.bib

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All documentation is copyright its authors; we didn't write any of that.