Files in mskilab/gGnome
gGnome: reference based assembly graph for analyzing rearranged genomes
.DS_Store
.Rbuildignore
.github/.gitignore
.github/workflows/check-release.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/CPX_matrix.R
R/PGVdb.R
R/Rcplex.R
R/apps.R
R/control.R
R/converters.R
R/eventCallers.R
R/gGnome.R
R/gurobi.R
R/jsUtils.R
R/misc_utils.R
R/test.json
R/test_CPLEX.R
R/utils.R
README.md
_pkgdown.yml
articles/gGnome.png
articles/tutorial.Rmd
codecov.yml
configure
docs/.nojekyll
docs/404.html
docs/LICENSE-text.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Junction-class-constructor.html
docs/reference/Junction.html
docs/reference/Junction.over.html
docs/reference/Junction.subset.html
docs/reference/Rplot001.png
docs/reference/amp.html
docs/reference/balance.html
docs/reference/bcheck.html
docs/reference/binstats.html
docs/reference/c.gGraph.html
docs/reference/c.html
docs/reference/cbind.html
docs/reference/chromoplexy.html
docs/reference/chromothripsis.html
docs/reference/colnames2.html
docs/reference/convertEdges.html
docs/reference/copy3.html
docs/reference/cougar2gg.html
docs/reference/dedup.cols.html
docs/reference/del.html
docs/reference/dim.html
docs/reference/dt_na2false.html
docs/reference/dup.html
docs/reference/duped.html
docs/reference/duplicated.matrix.html
docs/reference/enframe_list.html
docs/reference/equals.gGraph.html
docs/reference/events.html
docs/reference/events.to.gr.html
docs/reference/fitcn.html
docs/reference/fusions.html
docs/reference/gEdge.html
docs/reference/gEdge.in.html
docs/reference/gEdge.over.html
docs/reference/gG.html
docs/reference/gGnome.html
docs/reference/gGnome.js.html
docs/reference/gGraph-constructor.html
docs/reference/gGraph.html
docs/reference/gGraph.subset.html
docs/reference/gNode-over.html
docs/reference/gNode-subset.html
docs/reference/gNode.html
docs/reference/gNode.loose.html
docs/reference/gW.html
docs/reference/gWalk.html
docs/reference/gWalk.over.html
docs/reference/gWalk.subset.html
docs/reference/gdist.html
docs/reference/gr.noval.html
docs/reference/gr.spreduce.html
docs/reference/grapes-K-grapes.html
docs/reference/haplograph.html
docs/reference/index.html
docs/reference/initialize.html
docs/reference/internal.html
docs/reference/intersect.Junction.html
docs/reference/intersect.gEdge.html
docs/reference/intersect.gNode.html
docs/reference/isNA.html
docs/reference/jJ.html
docs/reference/karyotype.html
docs/reference/label.runs.html
docs/reference/length.html
docs/reference/lengths.html
docs/reference/loosefix.html
docs/reference/match3.html
docs/reference/merge.Junction.html
docs/reference/merge.html
docs/reference/merge.repl.html
docs/reference/microhomology.html
docs/reference/na2false.html
docs/reference/peel.html
docs/reference/pgv.html
docs/reference/phased.binstats.html
docs/reference/ploidy.html
docs/reference/proximity.html
docs/reference/qrp.html
docs/reference/ra.duplicated.html
docs/reference/ra.merge.html
docs/reference/rand.string.html
docs/reference/read.juncs.html
docs/reference/read_cmap.html
docs/reference/read_xmap.html
docs/reference/reciprocal.html
docs/reference/refresh.html
docs/reference/rel2abs.html
docs/reference/rep_len2.html
docs/reference/rleseq.html
docs/reference/rowMaxs.html
docs/reference/rowMins.html
docs/reference/run_gurobi.html
docs/reference/seq_along2.html
docs/reference/seqinfo.html
docs/reference/seqlengths.html
docs/reference/seqlevels.html
docs/reference/setcols.html
docs/reference/setdiff.html
docs/reference/setxor.html
docs/reference/simple.html
docs/reference/sparse_subset.html
docs/reference/split.gGraph.html
docs/reference/spmelt.html
docs/reference/sub-.Junction.html
docs/reference/sub-.gEdge.html
docs/reference/sub-.gNode.html
docs/reference/sub-.gWalk.html
docs/reference/sum.gGraph.html
docs/reference/tic.html
docs/reference/transplant.html
docs/reference/union.html
docs/reference/unique.html
docs/reference/vaggregate.html
docs/reference/width.html
docs/sitemap.xml
inst/extdata/COLO_668.jabba.simple.rds
inst/extdata/EFO_21.jabba.simple.rds
inst/extdata/H838_rare_variant_pipeline_EXP_REFINEFINAL1_bionano.xmap.gz
inst/extdata/HARA.jabba.simple.rds
inst/extdata/HCC1143.js
inst/extdata/HCC1143.svaba.somatic.sv.vcf
inst/extdata/HCC827.jabba.simple.rds
inst/extdata/HGC_27.jabba.simple.rds
inst/extdata/JHOS_2.jabba.simple.rds
inst/extdata/KYSE_410.jabba.simple.rds
inst/extdata/LK_2.jabba.simple.rds
inst/extdata/MFE_280.jabba.simple.rds
inst/extdata/NCI_H1105.jabba.simple.rds
inst/extdata/NCI_H2081.jabba.simple.rds
inst/extdata/NCI_H2228.jabba.simple.rds
inst/extdata/NCI_H526.jabba.simple.rds
inst/extdata/SCLC_21H.jabba.simple.rds
inst/extdata/SNU_119.jabba.simple.rds
inst/extdata/coverage.5k.txt
inst/extdata/cplex_codes.rds
inst/extdata/data.with.cn.json
inst/extdata/delly.final.vcf.gz
inst/extdata/filter.PE2.SR2.sv.vcf.gz
inst/extdata/gTrack.js/#data.json#
inst/extdata/genes.rds
inst/extdata/gw.grl.rds
inst/extdata/hcc1954.example.sg.rds
inst/extdata/hcc1954.rigma.phased.cn.rds
inst/extdata/hcc1954.rigma.sg.cn.rds
inst/extdata/hcc1954.rigma.sg.cov.rds
inst/extdata/hcc1954.rigma.sg.hets.rds
inst/extdata/hcc1954.rigma.sg.rds
inst/extdata/hcc1954.rigma.sg.with.pp.rds
inst/extdata/hcc1954/cougar
inst/extdata/hcc1954/hcc1954.chr8.cov.rds
inst/extdata/hcc1954/jabba.rds
inst/extdata/hcc1954/prego/chrm.map.tsv
inst/extdata/hcc1954/prego/intervalFile
inst/extdata/hcc1954/prego/intervalFile.graphml
inst/extdata/hcc1954/prego/intervalFile.results
inst/extdata/hcc1954/prego/variantFile
inst/extdata/hcc1954/remixt/breakpoints.tsv
inst/extdata/hcc1954/remixt/out.brk.tsv
inst/extdata/hcc1954/remixt/out.cn.tsv
inst/extdata/hcc1954/weaver/REGION_CN_PHASE
inst/extdata/hcc1954/weaver/SV_CN_PHASE
inst/extdata/hcc1954/weaver/SV_REMOVED
inst/extdata/hcc1954/weaver/SV_SELECTED
inst/extdata/hg19.cytoband.txt
inst/extdata/hg19.regularChr.chrom.sizes
inst/extdata/human_g1k_v37.chrom.sizes
inst/extdata/human_g1k_v37.regular.chrom.sizes
inst/extdata/intervalFile
inst/extdata/intervalFile.graphml
inst/extdata/intervalFile.results
inst/extdata/jabba.ref.rds
inst/extdata/jabba.simple.rds
inst/extdata/jsUtils/mock_ref_dir/genes.json
inst/extdata/jsUtils/mock_ref_dir/metadata.json
inst/extdata/jsUtils/phylogeny.newick
inst/extdata/junctions.bedpe
inst/extdata/microhomology.test.fasta
inst/extdata/microhomology/ex1/jj.grl.rds
inst/extdata/microhomology/ex1/ref.fasta
inst/extdata/microhomology/ex2/jj.grl.rds
inst/extdata/microhomology/ex2/ref.fasta
inst/extdata/novoBreak.pass.flt.vcf
inst/extdata/ont.subset.bedpe
inst/extdata/ont.subset.vcf
inst/extdata/phylogeny-pgv.newick
inst/extdata/rck.hcc1954.tar.gz
inst/extdata/remixt/breakpoints.tsv
inst/extdata/remixt/out.brk.tsv
inst/extdata/remixt/out.cn.tsv
inst/extdata/rpexample.rds
inst/extdata/svaba.subset.junction.rds
inst/extdata/svaba.subset.vcf
inst/extdata/test.gtf
inst/extdata/testing.es.rds
inst/extdata/testing.segs.rds
inst/extdata/testing_cov.rds
inst/extdata/testing_junctions.rds
inst/extdata/testing_tile.rds
inst/extdata/testing_win.rds
inst/extdata/tutorial/gGnome.js.screenshot.png
inst/extdata/walks.gg.rds
inst/extdata/weaver/REGION_CN_PHASE
inst/extdata/weaver/SV_CN_PHASE
man/Junction-class-constructor.Rd
man/Junction.Rd
man/Junction.over.Rd
man/Junction.subset.Rd
man/amp.Rd
man/balance.Rd
man/bcheck.Rd
man/binstats.Rd
man/c.Rd
man/c.gGraph.Rd
man/cbind.Rd
man/chromoplexy.Rd
man/chromothripsis.Rd
man/colnames2.Rd
man/convertEdges.Rd
man/copy3.Rd
man/cougar2gg.Rd
man/dedup.cols.Rd
man/del.Rd
man/dim.Rd
man/dt_na2false.Rd
man/dup.Rd
man/duped.Rd
man/duplicated.matrix.Rd
man/enframe_list.Rd
man/equals.gGraph.Rd
man/events.Rd
man/events.to.gr.Rd
man/fitcn.Rd
man/fusions.Rd
man/gEdge.Rd
man/gEdge.in.Rd
man/gEdge.over.Rd
man/gG.Rd
man/gGnome.Rd
man/gGnome.js.Rd
man/gGraph-constructor.Rd
man/gGraph.Rd
man/gGraph.subset.Rd
man/gNode-over.Rd
man/gNode-subset.Rd
man/gNode.Rd
man/gNode.loose.Rd
man/gW.Rd
man/gWalk.Rd
man/gWalk.over.Rd
man/gWalk.subset.Rd
man/gdist.Rd
man/gr.noval.Rd
man/gr.spreduce.Rd
man/grapes-K-grapes.Rd
man/haplograph.Rd
man/initialize.Rd
man/internal.Rd
man/intersect.Junction.Rd
man/intersect.gEdge.Rd
man/intersect.gNode.Rd
man/isNA.Rd
man/jJ.Rd
man/karyotype.Rd
man/label.runs.Rd
man/length.Rd
man/lengths.Rd
man/loosefix.Rd
man/match3.Rd
man/merge.Junction.Rd
man/merge.Rd
man/merge.repl.Rd
man/microhomology.Rd
man/na2false.Rd
man/peel.Rd
man/pgv.Rd
man/phased.binstats.Rd
man/ploidy.Rd
man/proximity.Rd
man/ra.duplicated.Rd
man/ra.merge.Rd
man/rand.string.Rd
man/read.juncs.Rd
man/read_cmap.Rd
man/read_xmap.Rd
man/reciprocal.Rd
man/refresh.Rd
man/rel2abs.Rd
man/rep_len2.Rd
man/rleseq.Rd
man/rowMaxs.Rd
man/rowMins.Rd
man/run_gurobi.Rd
man/seq_along2.Rd
man/seqinfo.Rd
man/seqlengths.Rd
man/seqlevels.Rd
man/setcols.Rd
man/setdiff.Rd
man/setxor.Rd
man/simple.Rd
man/sparse_subset.Rd
man/split.gGraph.Rd
man/spmelt.Rd
man/sub-.Junction.Rd
man/sub-.gEdge.Rd
man/sub-.gNode.Rd
man/sub-.gWalk.Rd
man/sum.gGraph.Rd
man/tic.Rd
man/transplant.Rd
man/union.Rd
man/unique.Rd
man/vaggregate.Rd
man/width.Rd
old.travis.yml
srcs/src.blank/Makevars
srcs/src.blank/Makevars.in
srcs/src.blank/Makevars.win
srcs/src.blank/Rcplex2.c
srcs/src.blank/Rcplex2.h
srcs/src.rcplex/Makevars
srcs/src.rcplex/Makevars.win
srcs/src.rcplex/Rcplex2.c
srcs/src.rcplex/Rcplex2.h
srcs/src.rcplex/Rcplex_params.c
srcs/src.rcplex/Rcplex_utils.c
tests/testthat.R
tests/testthat/test_gGnome_balance.R
tests/testthat/test_gGnome_converters.R
tests/testthat/test_gGnome_event_callers.R
tests/testthat/test_gGnome_ops.R
tests/testthat/test_gGnome_peel.R
tests/testthat/test_gGnome_utils.R
tests/testthat/test_jsUtils.R
