Files in daewoooo/SVbyEye
Visualization of genomic structural variants
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/R-CMD-check.yaml.save
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/addAlignments.R
R/addAnnotation.R
R/addSelfAlignments.R
R/breakPafAlignment.R
R/cigarUtils.R
R/disjoinPafAlignments.R
R/filterPaf.R
R/flipPaf.R
R/geom_arrowhead.R
R/geom_miropeats.R
R/geom_roundrect.R
R/geom_wide_arc.R
R/getSequenceContent.R
R/global.R
R/helpers.R
R/liftRangesToAlignment.R
R/maskFasta.R
R/nucmerToPaf.R
R/pafAlignmentToBins.R
R/pafToCoords.R
R/pafToFasta.R
R/pafToGaps.R
R/plotAVA.R
R/plotDotp.R
R/plotGenome.R
R/plotMiro.R
R/plotSelf.R
R/readPaf.R
R/regionsToFasta.R
R/subsetPafAlignments.R
R/syncRangesDir.R
R/timedMessage.R
R/utils-pipe.R
README.md
SVbyEye.Rproj
inst/extdata/HG00438_1_nucmer.coords
inst/extdata/HG01071_2_mm2.paf
inst/extdata/PTR_test.paf
inst/extdata/test1.paf
inst/extdata/test1.sd.annot.RData
inst/extdata/test1_query_annot.txt
inst/extdata/test1_target_annot.txt
inst/extdata/test2.paf
inst/extdata/test2.sd.annot.RData
inst/extdata/test3.paf
inst/extdata/test4.paf
inst/extdata/test4_query.fasta
inst/extdata/test_annot_ava.RData
inst/extdata/test_ava.paf
inst/extdata/test_getFASTA.paf
inst/extdata/test_getFASTA_query.fasta
inst/extdata/test_getFASTA_query.fasta.fai
inst/extdata/test_lift1.paf
inst/extdata/test_lift2.paf
man/StatMiropeats.Rd
man/StatWideArc.Rd
man/add.control.points.Rd
man/addAlignments.Rd
man/addAnnotation.Rd
man/addSelfAlignments.Rd
man/breakPaf.Rd
man/breakPafAlignment.Rd
man/cigar2ranges.Rd
man/collapsePaf.Rd
man/disjoinPafAlignments.Rd
man/doc/SVbyEye.html
man/fasta2nucleotideContent.Rd
man/figures/SVbyEye_online.png
man/filterPaf.Rd
man/flipPaf.Rd
man/flipQueryAnnotation.Rd
man/geom_arrowhead.Rd
man/geom_miropeats.Rd
man/geom_roundrect.Rd
man/geom_wide_arc.Rd
man/getAnnotationLevels.Rd
man/getColorScheme.Rd
man/getNucleotideContent.Rd
man/liftRangesToAlignment.Rd
man/maskFASTA.Rd
man/mirrorRanges.Rd
man/nucmer2PAF.Rd
man/paf2FASTA.Rd
man/paf2continuousScale.Rd
man/paf2coords.Rd
man/paf2gaps.Rd
man/paf2nucleotideContent.Rd
man/pafAlignmentToBins.Rd
man/pafToBins.Rd
man/parseCigarString.Rd
man/pipe.Rd
man/plotAVA.Rd
man/plotGenome.Rd
man/plotMiro.Rd
man/plotSelf.Rd
man/processPafTags.Rd
man/q2t.Rd
man/readPaf.Rd
man/regions2FASTA.Rd
man/reportGaps.Rd
man/simpledotplot.Rd
man/subsetPaf.Rd
man/subsetPafAlignments.Rd
man/syncRangesDir.Rd
tests/testthat.R
tests/testthat/chr12_17521907_18108016_misorient.paf
tests/testthat/test_breakPafAlignment.R
tests/testthat/test_geomAndPlottingWrappers.R
tests/testthat/test_liftRangesToAlignment.R
vignettes/SVbyEye.Rmd
vignettes/references.bib
