plot MMD distances
Find peaks with extreme count values
Example DBA object used to illustrate usage of the MMDiff package
DBAmmd Object for Cfp1 example
Compute distances between pairs of histograms
Extract data from DBAmmd objects
Peaks for Cfp1-data set
Example DBA object used to illustrate usage of the MMDiff package
Class DBAmmd
Statistical Testing for ChIP-Seq data sets
Compute Peak histograms
Compute p-values for each peak based on distances between histograms
Determine Normalisation factors
Add histograms (binned read enrichment profiles) to an existing
DBA object
compute p-values
Compute distances between Peaks
estimate center of fragments
plotDISTS4Peak
mm9-Genes
ui component for interactive visualization of MMD,GMD and Pearson Difference
as well as plotting peaks
Get reads from indexed bam files for defined regions
plot read enrichment profiles at a specific peak for all specified
samples.
Shiny Application for interactive visualization of MMD,GMD and
Pearson Difference as well as plotting peaks
report results
Generics for DBAmmd-Class
plotDists
Shiny server code for interactive visualization of MMD distances,
peak plots, and MMD distances by sample.