├── DESCRIPTION ├── NAMESPACE ├── R └── zroutines.R ├── README.md ├── configure ├── configure.ac ├── man ├── add.broad.peak.regions.Rd ├── densum.Rd ├── find.binding.positions.Rd ├── get.binding.characteristics.Rd ├── get.broad.enrichment.clusters.Rd ├── get.conservative.fold.enrichment.profile.Rd ├── get.conservative.fold.enrichment.profile2.Rd ├── get.mser.Rd ├── get.mser.interpolation.Rd ├── get.smoothed.enrichment.mle.Rd ├── get.smoothed.enrichment.mle2.Rd ├── get.smoothed.tag.density.Rd ├── output.binding.results.Rd ├── points.within.Rd ├── points_withinFunction.Rd ├── read.arachne.tags.Rd ├── read.bam.tags.Rd ├── read.bin.maqmap.tags.Rd ├── read.bowtie.tags.Rd ├── read.eland.tags.Rd ├── read.helicos.tags.Rd ├── read.maqmap.tags.Rd ├── read.meland.tags.Rd ├── read.short.arachne.tags.Rd ├── read.tagalign.tags.Rd ├── remove.local.tag.anomalies.Rd ├── select.informative.tags.Rd ├── spp-package.Rd ├── write.broadpeak.info.Rd ├── write.narrowpeak.binding.Rd └── writewig.Rd └── src ├── Makevars.in ├── api_global.h ├── bed2vector.cpp ├── cdensum.c ├── const.h ├── maqmap.c ├── maqmap.h ├── maqread.cpp ├── pc.h ├── peaks.cpp ├── spp_init.c └── wdl.cpp /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hms-dbmi/spp/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hms-dbmi/spp/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/zroutines.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hms-dbmi/spp/HEAD/R/zroutines.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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