chroGPS: chroGPS: visualizing the epigenome

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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.

Author
Oscar Reina, David Rossell
Date of publication
None
Maintainer
Oscar Reina <oscar.reina@irbbarcelona.org>
License
GPL (>=2.14)
Version
1.22.0

View on Bioconductor

Man pages

addVar
Plot vector of a quantitative variable over a MDS map.
adjustPeaks
Adjust peak width so that samples obtained under different...
boostMDS
Improve goodness-of-fit of a given MDS solution in terms of...
clusGPS
Computation of cluster density estimates for cluster contour...
clusGPS-class
Class '"clusGPS"'
distGPS
Compute matrix with pairwise distances between objects....
distGPS-class
Class '"distGPS"'
domainDist
Overview of intra and inter-domain distances.
geneSetGPS
Highlight point (gene) position over a Multi-dimensional...
getURL
Retrieve file from URL.
gff2RDList
Retrieve binding site information from GFF3 files.
gps2xgmml
Export an 'mds' object to Cytoscape .xgmml format
mds
Metric and non-metric Multidimensional Scaling for a distGPS...
mds-class
Class '"mds"'
mergeClusters
Unsupervised cluster merging based on their observed overlap...
procrustesAdj
Use Procrustes to adjust an MDS map containing samples...
profileClusters
Compute enrichment/depletion ratio for the observed...
s2
Sample binding site and related data from S2 and BG3 cell...
splitDistGPS-class
Class '"splitDistGPS"'

Files in this package

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