API for parklab/r-scan2
Single Cell ANalysis 2
| Global functions | |
|---|---|
| DEPRECATED_compute.spatial.sensitivity.depth | Source code |
| K.func | Source code |
| abmodel.approx.ctx | Source code |
| abmodel.approx.logp | Source code |
| abmodel.downsample.hsnps | Source code |
| abmodel.fit.one.chrom | Source code |
| abmodel.refine.parameter.space | Source code |
| abmodel.sample | Source code |
| abmodel.shrink.parameter.space | Source code |
| adjust.phase | Source code |
| alg3.2.2 | Source code |
| analysis.set.tiling | Source code |
| analysis.set.tiling.for.parallelization | Source code |
| analysis.set.tiling.for.parallelization.helper | Source code |
| analysis.set.tiling.helper | Source code |
| annotate.gatk | Source code |
| annotate.gatk.counts | Source code |
| annotate.gatk.lowmq | Source code |
| approx.abmodel.covariance | Source code |
| as.spectrum | Source code |
| bedtools.permute | Source code |
| binomial.effect.on.correlation | Source code |
| check.chunked | Source code |
| check.length | Source code |
| check.slots | Source code |
| chunked.fread | Source code |
| cigar.get.null.sites | Source code |
| classify.muts | Source code |
| compress.dt | Source code |
| compress.spatial.sens | Source code |
| compute.ab.given.sites.and.training.data | Source code |
| compute.callable.region | Source code |
| compute.cigar.scores | Source code |
| compute.filter.reasons | Source code |
| compute.spatial.sensitivity.abmodel | Source code |
| concat.perms | Source code |
| decompress.dt | Source code |
| digest.depth.2sample | Source code |
| genome.string.to.bsgenome.object | Source code |
| genome.string.to.chroms | Source code |
| genome.string.to.seqinfo.object | Source code |
| genome.string.to.tiling | Source code |
| get.3mer | Source code |
| get.autosomes | Source code |
| get.distance.distn | Source code |
| get.gbp.by.genome | Source code |
| get.high.quality.mutations | Source code |
| get.rscan2.version | Source code |
| get.sex.chroms | Source code |
| get.training.sites.for.abmodel | Source code |
| get.training.sites.for.abmodel.by.range | Source code |
| haploid.chroms | Source code |
| helper.ab.fits | Source code |
| helper.abmodel.cov | Source code |
| helper.build.info.string | Source code |
| helper.data | Source code |
| helper.plot.mutsig | Source code |
| helper.plot.mutsig.one | Source code |
| helper.plot.region | Source code |
| helper.vcf.header | Source code |
| id83 | Source code |
| infer.gp | Source code |
| infer.gp.block | Source code |
| infer.gp1 | Source code |
| is.id83 | Source code |
| is.sbs96 | Source code |
| join.phased.hsnps | Source code |
| load.summary | Source code |
| make.indel.perms.helper | Source code |
| make.integrated.table | Source code |
| make.perms | Source code |
| make.scan | Source code |
| make.snv.perms.helper | Source code |
| make.summary.scan2 | Source code |
| match.ab | Source code |
| model.somatic.sensitivity | Source code |
| parse.analysis.regions.to.granges | Source code |
| parse.static.filter.params | Source code |
| perfcheck | Source code |
| plot.ab | Source code |
| plot.fcontrol | Source code |
| plot.fdr | Source code |
| plot.id83 | Source code |
| plot.sbs96 | Source code |
| prehelper.plot.mutsig | Source code |
| quantize.raw1 | Source code |
| quantize.raw2 | Source code |
| read.binned.counts | Source code |
| read.cigar.data | Source code |
| read.config | Source code |
| read.depth.2sample | Source code |
| read.gatk.1sample | Source code |
| read.integrated.table.1sample | Source code |
| read.tabix.data | Source code |
| read.tabix.header | Source code |
| read.table.1sample | Source code |
| reduce.table | Source code |
| run.chunked.pipeline | Source code |
| run.pipeline | Source code |
| sbs96 | Source code |
| select.muttype.and.alleletype | Source code |
| select.perms | Source code |
| shared.classifier | Source code |
| tabix.read.only.cols | Source code |
| test.equal | Source code |
| test.output | Source code |
| test.tol | Source code |
| testpipe | Source code |
| unquantize.raw1 | Source code |
| unquantize.raw2 | Source code |
| vary.get.calls | Source code |
| vary.get.metrics | Source code |
| vary.static.filter.param | Source code |
| vary.target.fdr | Source code |
