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... |
get.broad.enrichment.clusters | Determine broad clusters of enrichment |
get.conservative.fold.enrichment.profile | Estimate minimal fold enrichment/depletion along the... |
get.conservative.fold.enrichment.profile2 | Return Conservative fold enrichment profile controlling for... |
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... |
get.smoothed.enrichment.mle2 | Calculate background input controlled chromosome-wide... |
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... |
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... |
select.informative.tags | Choose informative tags |
spp-package | ChIP-seq (Solexa) Processing Pipeline |
write.broadpeak.info | Write out determined broad enrichment regions using broadPeak... |
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... |
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