Files in jmonlong/PopSV
Population-based detection of structural variants from Read-Depth signal
.gitignore
.travis.yml
1-BasicWorkflow.md
2-ClusterManagement-BatchJobs.md
2-ClusterManagement.md
3-Visualization.md
4-Cancer.md
5-FAQ.md
6-Publication.md
9-About.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/BatchJobs_profile.R
scripts/BatchJobs/README.md
scripts/BatchJobs/abacus.tmpl
scripts/BatchJobs/automatedPipeline-BatchJobs.R
scripts/BatchJobs/guillimin.tmpl
scripts/BatchJobs/makeClusterFunctionsAdaptive.R
scripts/BatchJobs/run-PopSV-XY-batchjobs-automatedPipeline.R
scripts/BatchJobs/run-PopSV-batchjobs-automatedPipeline.R
scripts/BatchJobs/run-PopSV-batchjobs.R
scripts/README.md
scripts/batchtools/README.md
scripts/batchtools/automatedPipeline-batchtools.R
scripts/batchtools/batchtools.conf.R
scripts/batchtools/batchtools.conf.local.R
scripts/batchtools/batchtools.conf.torque.R
scripts/batchtools/batchtools.slurm.tmpl
scripts/batchtools/batchtools.torque.tmpl
scripts/batchtools/run-PopSV-batchtools-automatedPipeline-fromCounts.R
scripts/batchtools/run-PopSV-batchtools-automatedPipeline.R
scripts/batchtools/test-batchtools.R
scripts/binBigWig.py
scripts/postCallingAnalysis.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
