API for hms-dbmi/spp
ChIP-Seq Processing Pipeline
| Global functions | |
|---|---|
| add.broad.peak.regions | Man page Source code |
| binomial.proportion.ratio.bounds | Source code |
| calculate.enrichment.estimates | Source code |
| chain.to.reference.comparison | Source code |
| dataset.density.ratio | Source code |
| dataset.density.size | Source code |
| densum | Man page Source code |
| determine.lwcc.threshold | Source code |
| filter.binding.sites | Source code |
| filter.singular.positions.by.local.density | Source code |
| find.binding.positions | Man page Source code |
| find.significantly.enriched.regions | Source code |
| generate.randomized.data | Source code |
| get.binding.characteristics | Man page Source code |
| get.broad.enrichment.clusters | Man page Source code |
| get.clusters2 | Source code |
| get.conservative.fold.enrichment.profile | Man page Source code |
| get.conservative.fold.enrichment.profile2 | Man page Source code |
| get.eval.fdr.vectors | Source code |
| get.mser | Man page Source code |
| get.mser.interpolation | Man page Source code |
| get.relative.coordinates | Source code |
| get.smoothed.enrichment.mle | Man page Source code |
| get.smoothed.enrichment.mle2 | Man page Source code |
| get.smoothed.tag.density | Man page Source code |
| get.subsample.chain.calls | Source code |
| lwcc | Source code |
| lwcc.prediction | Source code |
| mbs.enrichment.bounds | Source code |
| mser.chain.interpolation | Source code |
| old.dataset.density.ratio | Source code |
| output.binding.results | Man page Source code |
| points.within | Man page Source code |
| points_withinFunction | Man page Source code |
| read.arachne.tags | Man page Source code |
| read.bam.tags | Man page Source code |
| read.bin.maqmap.tags | Man page Source code |
| read.bowtie.tags | Man page Source code |
| read.eland.tags | Man page Source code |
| read.helicos.tags | Man page Source code |
| read.maqmap.tags | Man page Source code |
| read.meland.tags | Man page Source code |
| read.short.arachne.tags | Man page Source code |
| read.tagalign.tags | Man page Source code |
| regionset.intersection.c | Source code |
| remove.local.tag.anomalies | Man page Source code |
| remove.tag.anomalies | Source code |
| select.informative.tags | Man page Source code |
| show.scc | Source code |
| spp | Man page |
| spp-package | Man page |
| t.find.min.saturated.enr | Source code |
| t.plotavcc | Source code |
| t.plotavccl | Source code |
| t.plotcc | Source code |
| t.plotchrcc | Source code |
| t.plotchrccl | Source code |
| t.precalculate.ref.peak.agreement | Source code |
| tag.block.shuffle | Source code |
| tag.enrichment.clusters | Source code |
| tag.lwcc | Source code |
| tag.scc | Source code |
| tag.wtd | Source code |
| window.call.mirror.binding | Source code |
| window.chr.call.mirror.binding | Source code |
| window.tag.count | Source code |
| window.tag.count.around | Source code |
| write.broadpeak.info | Man page Source code |
| write.narrowpeak.binding | Man page Source code |
| write.probe.wig | Source code |
| writewig | Man page Source code |
| wtd | Source code |
