GMD: Generalized Minimum Distance of distributions

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GMD is a package for non-parametric distance measurement between two discrete frequency distributions.

Author
Xiaobei Zhao [aut, cre, cph], Albin Sandelin [aut]
Date of publication
2014-08-27 14:29:53
Maintainer
Xiaobei Zhao <xiaobei@binf.ku.dk>
License
GPL (>= 2)
Version
0.3.3
URLs

View on CRAN

Man pages

bedgraph.to.depth
Convert a BedGraph fiel to a vector of depth-like signals
cage
CAGE Data: Transcription Start Site Distributions (TSSDs) by...
chipseq
ChIP-seq data: ChIP-seq Enrichment around TSSs
css
Clustering Sum-of-Squares for clustering evaluation
elbow
The "Elbow" Method for Clustering Evaluation
equalize.list
Make members of a list equal size
gdist
Generalized Distance Matrix Computation
get.sep
Get row or column lines of separation for heatmap.3
ghist
Generalized Histogram Computation
gmdm
Generalized Minimum Distance Matrix
gmdp
Generalized Minimum Distance between a pair of distributions
GMD-package
The Package for Generalized Minimum Distance (GMD)...
heatmap.3
Enhanced Heatmap Representation with Dendrogram and Partition
legend
Add Legends to Plots
mhist.summary
Bin-wise summary of histograms
plot.gmdm
S3 method for class 'gmdm'
plot.gmdp
Plot function for class gmdp
plot.mhist
S3 method for class 'mhist'.
ts2df
Convert time series to data frame

Files in this package

GMD
GMD/inst
GMD/inst/CITATION
GMD/inst/tests
GMD/inst/tests/GMD-demo.R
GMD/inst/extdata
GMD/inst/extdata/hg19
GMD/inst/extdata/hg19/H3K36me3.BedGraph.gz
GMD/inst/extdata/hg19/H3K27me3.BedGraph.gz
GMD/inst/extdata/hg19/H3K9me3.BedGraph.gz
GMD/inst/extdata/hg19/H3K4me2.BedGraph.gz
GMD/inst/extdata/hg19/H3K4me1.BedGraph.gz
GMD/inst/extdata/hg19/H3K4me3.BedGraph.gz
GMD/inst/doc
GMD/inst/doc/GMD-data-processing.Rnw
GMD/inst/doc/GMD-vignette.pdf
GMD/inst/doc/GMD-vignette.Rnw
GMD/inst/doc/GMD-data-processing.pdf
GMD/inst/doc/GMD-vignette.R
GMD/inst/doc/GMD-data-processing.R
GMD/src
GMD/src/base.h
GMD/src/gmd.h
GMD/src/gmd.c
GMD/NAMESPACE
GMD/demo
GMD/demo/00Index
GMD/demo/GMD-demo.R
GMD/NEWS
GMD/data
GMD/data/cage.RData
GMD/data/chipseq_hCD4T.RData
GMD/data/chipseq_mES.RData
GMD/data/cagel.RData
GMD/R
GMD/R/GMD-data.R
GMD/R/ghist.R
GMD/R/heatmap3.R
GMD/R/GMD-package.R
GMD/R/css.R
GMD/R/GMD-internal.R
GMD/R/gmdp.R
GMD/R/util.R
GMD/R/gdist.R
GMD/R/gmdm.R
GMD/R/imports.R
GMD/vignettes
GMD/vignettes/GMD-data-processing.Rnw
GMD/vignettes/bioinfo.sty
GMD/vignettes/fig
GMD/vignettes/fig/GMD-fig-case-nottem-01.pdf
GMD/vignettes/fig/GMD-fig-example-ghist-02.pdf
GMD/vignettes/fig/GMD-fig-example-ghist-01b.pdf
GMD/vignettes/fig/GMD-fig-example-GMD-01.pdf
GMD/vignettes/fig/GMD-fig-example-ghist-01.pdf
GMD/vignettes/fig/GMD-fig-case-chipseq-01.pdf
GMD/vignettes/fig/GMD-fig-case-chipseq-02.pdf
GMD/vignettes/fig/GMD-fig-example-heatmap3b-01.pdf
GMD/vignettes/fig/hg19-RPS13-histone.pdf
GMD/vignettes/fig/GMD-fig-example-css-01.pdf
GMD/vignettes/fig/GMD-fig-example-gclust-01.pdf
GMD/vignettes/fig/GMD-fig-example-heatmap3a-01.pdf
GMD/vignettes/fig/GMD-fig-case-iris-01.pdf
GMD/vignettes/fig/GMD-fig-example-gdist-01.pdf
GMD/vignettes/fig/GMD-fig-case-cage-02.pdf
GMD/vignettes/fig/GMD-fig-case-cage-01.pdf
GMD/vignettes/R
GMD/vignettes/R/example-gdist.R
GMD/vignettes/R/example-GMD.R
GMD/vignettes/R/example-ghist.R
GMD/vignettes/R/example-heatmap3b.R
GMD/vignettes/R/hello-GMD.R
GMD/vignettes/R/case-nottem.R
GMD/vignettes/R/example-css.R
GMD/vignettes/R/case-chipseq.R
GMD/vignettes/R/example-heatmap3a.R
GMD/vignettes/R/case-cage.R
GMD/vignettes/R/case-iris.R
GMD/vignettes/GMD-vignette.Rnw
GMD/vignettes/Xvignette.sty
GMD/vignettes/GMD.bib
GMD/MD5
GMD/build
GMD/build/vignette.rds
GMD/DESCRIPTION
GMD/man
GMD/man/GMD-package.Rd
GMD/man/gmdp.Rd
GMD/man/heatmap.3.Rd
GMD/man/legend.Rd
GMD/man/css.Rd
GMD/man/mhist.summary.Rd
GMD/man/bedgraph.to.depth.Rd
GMD/man/ts2df.Rd
GMD/man/chipseq.Rd
GMD/man/elbow.Rd
GMD/man/plot.mhist.Rd
GMD/man/plot.gmdm.Rd
GMD/man/cage.Rd
GMD/man/gmdm.Rd
GMD/man/gdist.Rd
GMD/man/get.sep.Rd
GMD/man/plot.gmdp.Rd
GMD/man/ghist.Rd
GMD/man/equalize.list.Rd
GMD/.Rinstignore