addVar                  Plot vector of a quantitative variable over a
                        MDS map.
adjustPeaks             Adjust peak width so that samples obtained
                        under different conditions become comparable.
boostMDS                Improve goodness-of-fit of a given MDS solution
                        in terms of R-square.
clusGPS                 Computation of cluster density estimates for
                        cluster contour representation and
                        correct-classification rates (cluster
                        robustness). A pre-computed clustering of
                        elements used in the map has to be given as an
                        input, which is useful to explore results using
                        different clustering algorithms and
                        methodologies (top-down, bottom-up, etc).
clusGPS-class           Class '"clusGPS"'
distGPS                 Compute matrix with pairwise distances between
                        objects. Several GPS metrics are available.
distGPS-class           Class '"distGPS"'
domainDist              Overview of intra and inter-domain distances.
geneSetGPS              Highlight point (gene) position over a
                        Multi-dimensional Scaling plot.
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 object.
mds-class               Class '"mds"'
mergeClusters           Unsupervised cluster merging based on their
                        observed overlap with automatic changepoint
                        detection.
procrustesAdj           Use Procrustes to adjust an MDS map containing
                        samples obtained under different conditions,
                        e.g. technology or genetic backgrounds.
profileClusters         Compute enrichment/depletion ratio for the
                        observed epigenetic profiles in epigenetic
                        clusters.
s2                      Sample binding site and related data from S2
                        and BG3 cell lines in Drosophila melanogaster.
splidDistGPS-class      Class '"splitDistGPS"'
