Files in edsgard/scphaser

Phase Variants Within Genes Using Allele Counts

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/data.R R/performance.R R/scphaser.R README.md cran-comments.md data-raw/borel.R data-raw/humantcell.R data-raw/marinov.R data-raw/mousehybrid.R data-raw/read_rpkmfiles.R

data/marinov.rda

data/mousehybrid.rda

ignore/code/analysis/borel/ac2mat.R ignore/code/analysis/borel/ase2nvars.R ignore/code/analysis/borel/feat2diff.R

ignore/code/analysis/borel/log.sh

ignore/code/analysis/borel/ncells2ngenes.R ignore/code/analysis/borel/ncells2ngenes.exonic.R ignore/code/analysis/borel/ngenes.R ignore/code/analysis/borel/nvars2ngenes.R ignore/code/analysis/borel/phase.R ignore/code/analysis/borel/post.phase.R ignore/code/analysis/borel/seqdepth2ngenes.R

ignore/code/analysis/borel/snpase.downsamp_vars.sh

ignore/code/analysis/borel/snpase.sh

ignore/code/analysis/borel/stats.R ignore/code/analysis/combo/ase2nvars.R ignore/code/analysis/humantcell/params2sens.R ignore/code/analysis/humantcell/phase.R ignore/code/analysis/marinov/ac2knownhap.R

ignore/code/analysis/marinov/ase.bl6cast.sh

ignore/code/analysis/marinov/ase2nvars.R ignore/code/analysis/marinov/hap2refaltcount.R

ignore/code/analysis/marinov/log.sh

ignore/code/analysis/marinov/params2perf.R ignore/code/analysis/marinov/phase.R ignore/code/analysis/marinov/post.phase.R

ignore/code/analysis/marinov/prep.snps.sh

ignore/code/analysis/marinov/samplefilter.R

ignore/code/analysis/marinov/setdiff.py

ignore/code/analysis/marinov/snp2hapalleles.py

ignore/code/analysis/marinov/snpase.sh

ignore/code/analysis/mousehybrid/ac2mat.R ignore/code/analysis/mousehybrid/ase2nvars.R ignore/code/analysis/mousehybrid/bulk.R ignore/code/analysis/mousehybrid/complexity.R

ignore/code/analysis/mousehybrid/log.sh

ignore/code/analysis/mousehybrid/mousehybrid.R ignore/code/analysis/mousehybrid/ncells2ngenes.R ignore/code/analysis/mousehybrid/ncells2ngenes.downsample_vars.R ignore/code/analysis/mousehybrid/ngenes.R ignore/code/analysis/mousehybrid/nvars2ngenes.R ignore/code/analysis/mousehybrid/params2perf.R ignore/code/analysis/mousehybrid/params2sens.R ignore/code/analysis/mousehybrid/seqdepth2ngenes.R ignore/code/analysis/mousehybrid/seqdepth2ngenes.downsampled_vars_cells.R

ignore/code/analysis/mousehybrid/snpase.sh

ignore/code/analysis/performance.R ignore/code/debug.R ignore/code/excluded.R ignore/code/pkg.R ignore/code/stubs.R ignore/code/vignettes/meta.Rmd ignore/code/vignettes/scphaser.R ignore/code/vignettes/scphaser.Rmd ignore/code/vignettes/test.R ignore/code/vignettes/test.Rmd ignore/code/vignettes/vignette_template.Rmd ignore/res/borel/pdf/nallelecount2fracgenes.pdf ignore/res/borel/pdf/nallelecount2ngenes.pdf ignore/res/borel/pdf/ncells2fracgenes.replace_no.intronic_no.pdf ignore/res/borel/pdf/ncells2fracgenes.replace_no.pdf ignore/res/borel/pdf/ncells2ngenes.pdf ignore/res/borel/pdf/ncells2ngenes.replace_no.intronic_no.pdf ignore/res/borel/pdf/ncells2ngenes.replace_no.pdf ignore/res/borel/pdf/neighvar2dist.cds.dens.adobed.pdf ignore/res/borel/pdf/neighvar2dist.cds.dens.pdf ignore/res/borel/pdf/neighvar2dist.dna.dens.adobed.pdf ignore/res/borel/pdf/neighvar2dist.dna.dens.pdf ignore/res/borel/pdf/neighvar2dist.dna_cds.dens.adobed.pdf ignore/res/borel/pdf/neighvar2dist.hist.adobed.pdf ignore/res/borel/pdf/neighvar2dist.hist.pdf ignore/res/borel/pdf/nvars2fracgenes.pdf ignore/res/borel/pdf/nvars2ngenes.pdf ignore/res/combo/pdf/ase2nvars.dens.pdf ignore/res/combo/pdf/ase2nvars.dens.wbulk.pdf ignore/res/combo/pdf/cell2nreads_refseq.dens.adobed.pdf ignore/res/combo/pdf/cell2nreads_refseq.dens.pdf ignore/res/combo/pdf/gene2mean_refseq.freqpoly.adobed.pdf ignore/res/combo/pdf/gene2mean_refseq.freqpoly.pdf ignore/res/humantcell/pdf/ncells2ngenes.adobed.pdf ignore/res/humantcell/pdf/ncells2ngenes.pdf ignore/res/humantcell/pdf/phasetime.bar.pdf

ignore/res/humantcell/rds/humantcell.rda

ignore/res/humantcell/rds/phased.acset.rds

ignore/res/marinov/data/filt_vcfphased_randomase/monoase_0.05/param2perf.rds

ignore/res/marinov/data/filt_vcfphased_randomase/monoase_0.1/param2perf.rds

ignore/res/marinov/data/filt_vcfphased_randomase/monoase_0.2/param2perf.rds

ignore/res/marinov/pdf/filt_vcfphased/bak/feat.perf.pdf ignore/res/marinov/pdf/filt_vcfphased/bak/param2ngenes.pdf ignore/res/marinov/pdf/filt_vcfphased/bak/param2nvars.pdf ignore/res/marinov/pdf/filt_vcfphased/bak/var.perf.adobed.pdf ignore/res/marinov/pdf/filt_vcfphased/feat.perf.adobed.pdf ignore/res/marinov/pdf/filt_vcfphased/monoase_0/feat.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased/monoase_0/feat.n.pdf ignore/res/marinov/pdf/filt_vcfphased/monoase_0/var.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased/monoase_0/var.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/feat.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/feat.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/frac.vars.err.mouse_human.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.05/feat.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.05/feat.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.05/var.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.05/var.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.1/feat.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.1/feat.frac.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.1/feat.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.1/var.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.1/var.frac.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.1/var.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.2/feat.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.2/feat.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.2/var.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.2/var.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.5/feat.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.5/feat.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.5/var.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/monoase_0.5/var.n.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/perf.adobed.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/var.frac.err.pdf ignore/res/marinov/pdf/filt_vcfphased_randomase/var.n.pdf

ignore/res/mousehybrid/complexity/data/timing.rand.rds

ignore/res/mousehybrid/complexity/data/timing.rds

ignore/res/mousehybrid/complexity/pdf/time2ncells.adobed.pdf ignore/res/mousehybrid/complexity/pdf/time2ncells.pdf ignore/res/mousehybrid/complexity/pdf/time2ncells.scaled.pdf ignore/res/mousehybrid/complexity/pdf/time2ngenes.adobed.pdf ignore/res/mousehybrid/complexity/pdf/time2ngenes.pdf ignore/res/mousehybrid/complexity/pdf/time2ngenes.scaled.pdf ignore/res/mousehybrid/complexity/pdf/time2nvars.pdf ignore/res/mousehybrid/complexity/pdf/time2nvars.scaled.pdf

ignore/res/mousehybrid/perf/data/perf.full.rds

ignore/res/mousehybrid/perf/data/perf.ngenes_100.nparams_8.rds

ignore/res/mousehybrid/perf/data/perf.rds

ignore/res/mousehybrid/perf/pdf/ac.exhaust.TRUE/tpr.fpr.bar.adobed.pdf ignore/res/mousehybrid/perf/pdf/ac.exhaust.TRUE/tpr.fpr.bar.pdf ignore/res/mousehybrid/perf/pdf/filtparam2sens.adobed.pdf ignore/res/mousehybrid/perf/pdf/filtparam2sens.pdf ignore/res/mousehybrid/perf/pdf/frac.err.pdf ignore/res/mousehybrid/perf/pdf/mcc.adobed.pdf ignore/res/mousehybrid/perf/pdf/mcc.pdf ignore/res/mousehybrid/perf/pdf/nallelecount2fracgenes.pdf ignore/res/mousehybrid/perf/pdf/nallelecount2ngenes.pdf ignore/res/mousehybrid/perf/pdf/ncells2fracgenes.replace_no.pdf ignore/res/mousehybrid/perf/pdf/ncells2ngenes.adobed.pdf ignore/res/mousehybrid/perf/pdf/ncells2ngenes.pdf ignore/res/mousehybrid/perf/pdf/ncells2ngenes.replace_no.pdf ignore/res/mousehybrid/perf/pdf/ncells2ngenes.resampled.pdf ignore/res/mousehybrid/perf/pdf/nfeats_postfilt.pdf ignore/res/mousehybrid/perf/pdf/nvars2fracgenes.pdf ignore/res/mousehybrid/perf/pdf/nvars2ngenes.pdf ignore/res/mousehybrid/perf/pdf/nvars_postfilt.pdf ignore/res/mousehybrid/perf/pdf/perf.pdf ignore/res/test/conc.pdf

ignore/res/test/knitr-spin.html

ignore/res/test/knitr-spin.md ignore/res/test/rnd_conc.pdf

ignore/revdep/checks.rds

inst/CITATION

inst/doc/LICENSE

inst/doc/refman.pdf inst/doc/scphaser.R inst/doc/scphaser.Rmd

inst/doc/scphaser.html

man/call_gt.Rd man/filter_acset.Rd man/filter_feat_nminvar.Rd man/filter_homovars.Rd man/filter_var_gt.Rd man/filter_zerorow.Rd man/marinov.Rd man/mousehybrid.Rd man/new_acset.Rd man/phase.Rd man/plot_conc.Rd man/racset.Rd man/set_gt_conc.Rd man/subset_cols.Rd man/subset_feat.Rd man/subset_rows.Rd

scphaser.Rproj

tests/testthat.R tests/testthat/test-performance.R tests/testthat/test-phasing.R vignettes/scphaser.Rmd

edsgard/scphaser documentation built on May 15, 2019, 11:02 p.m.