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| spp-package | ChIP-seq (Solexa) Processing Pipeline |
| 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 | 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. |