add.broad.peak.regions
                        Calculate chromosome-wide profiles of smoothed
                        tag density
densum                  Do Something
find.binding.positions
                        Determine significant point protein binding
                        positions (peaks)
get.binding.characteristics
                        Calculate characteristics of observed
                        DNA-binding signal from cross-correlation
                        profiles
get.broad.enrichment.clusters
                        Determine broad clusters of enrichment
get.conservative.fold.enrichment.profile
                        Estimate minimal fold enrichment/depletion
                        along the chromosomes
get.conservative.fold.enrichment.profile2
                        Return Conservative fold enrichment profile
                        controlling for input and a single background
                        scale
get.mser                Calculate minimal saturated enrichment fold
                        ratio
get.mser.interpolation
                        Interpolate MSER dependency on the tag count
get.smoothed.enrichment.mle
                        Calculate chromosome-wide profiles of smoothed
                        enrichment estimate
get.smoothed.enrichment.mle2
                        Calculate background input controlled
                        chromosome-wide profiles of smoothed enrichment
                        estimate
get.smoothed.tag.density
                        Calculate chromosome-wide profiles of smoothed
                        tag density
output.binding.results
                        Write out determined binding peaks into a text
                        file table
points_within           Find points within
read.arachne.tags       Read in Arachne tags
read.bam.tags           Read BAM alignment file
read.bin.maqmap.tags    Read MAQ binary alignment map file
read.bowtie.tags        Read bowtie text alignment output file
read.eland.tags         Read eland output file
read.helicos.tags       Read in helicos tags
read.maqmap.tags        Read MAQ text alignment output file
read.meland.tags        Read modified BED tag alignment file that
                        contains variable match length information
read.short.arachne.tags
                        Read in ARACHNE short tags
read.tagalign.tags      Read in tagalign tags
remove.local.tag.anomalies
                        Restrict or remove positions with too many tags
                        relative to local background.
select.informative.tags
                        Choose informative tags
spp-package             ChIP-seq (Solexa) Processing Pipeline
write.broadpeak.info    Write out determined broad enrichment regions
                        using broadPeak format
write.narrowpeak.binding
                        Write out determined binding peaks using
                        narrowPeak format
writewig                A function to save a list of chromosome-wise
                        x/y data frames into a WIG file format.
