Files in jmonlong/PopSV
Population-based detection of structural variants from Read-Depth signal

.gitignore
.travis.yml
1-BasicWorkflow.md 2-ClusterManagement.md 3-Visualization.md 4-Cancer.md 5-FAQ.md 6-Publication.md
DESCRIPTION
NAMESPACE
R/PopSV-package.R R/aneuploidy.flag.R R/bin.bam.2d.R R/bin.bam.R R/bin.bw.R R/breakpoint.finder.interactive.R R/call.abnormal.cov.R R/chrplot.R R/chunk.bin.R R/cluster.regions.R R/cn.plot.R R/comp.index.files.R R/correct.GC.R R/coverage.plot.R R/coverage.plot.raw.R R/createEmptyDF.R R/draw.controls.R R/fdrtool.quantile.2N.R R/fdrtool.quantile.R R/filter.noncovered.bins.R R/find.comparable.bins.R R/fragment.genome.R R/fragment.genome.hg19.R R/freq.range.R R/gender.predict.R R/getGC.R R/getGC.hg19.R R/init.filenames.R R/localMax.R R/mean.sd.outlierR.R R/med.norm.R R/medvar.norm.R R/medvar.norm.internal.R R/mergeConsBin.cbs.R R/mergeConsBin.reduce.R R/mergeConsBin.simple.R R/mergeConsBin.z.R R/norm.tm.opt.R R/norm.z.quantile.R R/normQC.R R/pair.discordant.reads.R R/pca.norm.R R/qc.sample.R R/qc.samples.R R/qc.samples.cluster.R R/qc.zshift.unaffected.R R/quant.norm.R R/quick.count.R R/read.bedix.R R/samples.merge.R R/sv.summary.R R/sv.summary.interactive.R R/tmm.norm.R R/tn.norm.R R/tn.norm.qc.R R/tn.norm.qc.div.R R/tn.test.sample.R R/tnK.norm.R R/weight.ref.pca.R R/winsor.R R/write.split.samples.R R/writeVcf.R R/z.comp.R R/z.norm.R R/z.thres.cons.bins.R README.md TODO.md docs/ConstructingControlRegions.Rmd docs/ConstructingControlRegions.md
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-10-1.png
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-10-2.png
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-12-1.png
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-12-2.png
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-3-1.png
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-3-2.png
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-6-1.png
docs/ConstructingControlRegions_files/figure-markdown_github/unnamed-chunk-6-2.png
docs/README.md man/PopSV-package.Rd man/aneuploidy.flag.Rd man/bin.bam.2d.Rd man/bin.bam.Rd man/bin.bw.Rd man/breakpoint.finder.interactive.Rd man/call.abnormal.cov.Rd man/chrplot.Rd man/chunk.bin.Rd man/cluster.regions.Rd man/cn.plot.Rd man/comp.index.files.Rd man/correct.GC.Rd man/coverage.plot.Rd man/coverage.plot.raw.Rd man/createEmptyDF.Rd man/draw.controls.Rd man/fdrtool.quantile.2N.Rd man/fdrtool.quantile.Rd man/filter.noncovered.bins.Rd man/find.comparable.bins.Rd man/fragment.genome.Rd man/fragment.genome.hg19.Rd man/freq.range.Rd man/gender.predict.Rd man/getGC.Rd man/getGC.hg19.Rd man/init.filenames.Rd man/localMax.Rd man/mean.sd.outlierR.Rd man/med.norm.Rd man/medvar.norm.Rd man/medvar.norm.internal.Rd man/mergeConsBin.cbs.Rd man/mergeConsBin.reduce.Rd man/mergeConsBin.simple.Rd man/mergeConsBin.z.Rd man/norm.tm.opt.Rd man/normQC.Rd man/pair.discordant.reads.Rd man/pca.norm.Rd man/qc.sample.Rd man/qc.samples.Rd man/qc.samples.cluster.Rd man/qc.zshift.unaffected.Rd man/quant.norm.Rd man/quick.count.Rd man/read.bedix.Rd man/samples.merge.Rd man/sv.summary.Rd man/sv.summary.interactive.Rd man/tmm.norm.Rd man/tn.norm.Rd man/tn.norm.qc.Rd man/tn.norm.qc.div.Rd man/tn.test.sample.Rd man/tnK.norm.Rd man/weight.ref.pca.Rd man/winsor.Rd man/write.split.samples.Rd man/writeVcf.Rd man/z.comp.Rd man/z.norm.Rd man/z.thres.cons.bins.Rd
public/PopSVworkflow.png
public/bkptInteractive-trio.jpg
public/bkptInteractive.jpg
public/qcClustApp.png
public/svSummaryCN.png
public/svSummaryExport.png
public/svSummaryFreq.png
public/svSummaryNb.png
public/svSummaryNbSize.png
scripts/.BatchJobs.R scripts/automatedPipeline.R
scripts/binBigWig.py
scripts/guillimin.tmpl
scripts/makeClusterFunctionsAdaptive.R scripts/postCallingAnalysis.R scripts/run-PopSV-XY-batchjobs-automatedPipeline.R scripts/run-PopSV-XY-batchjobs.R scripts/run-PopSV-batchjobs-automatedPipeline.R scripts/run-PopSV-batchjobs.R scripts/run-PopSV-local.R
tests/dataForTests/NA12878_S1_chr18_1_1000000_s01.bam
tests/dataForTests/NA12878_S1_chr18_1_1000000_s01.bam.bai
tests/dataForTests/gc-hg19-chr18-30000-30100.bed.gz
tests/testthat.R tests/testthat/test-PVest.R tests/testthat/test-binbam.R tests/testthat/test-binning-gc.R tests/testthat/test-call.R tests/testthat/test-drawcontrols.R tests/testthat/test-freq.R tests/testthat/test-graphs.R tests/testthat/test-mergeBins.R tests/testthat/test-msdComp.R tests/testthat/test-norm.R tests/testthat/test-normqc.R tests/testthat/test-qcSamples.R tests/testthat/test-tabix.R tests/testthat/test-testcases.R tests/testthat/test-vcf.R tests/testthat/test-zcomp.R
jmonlong/PopSV documentation built on Oct. 20, 2017, 12:58 a.m.