Files in kullrich/CRBHits
Conditional reciprocal best hits (CRBHits) in R
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
.gitlab-ci.yml
.travis.yml
CODE_OF_CONDUCT.md
CRBHits.Rproj
DESCRIPTION
LICENSE
NAMESPACE
R/CRBHitsColors.R
R/aa2rbh.R
R/aadir2orthofinder.R
R/aafile2rbh.R
R/aly-data.R
R/ath-data.R
R/ath_aly_crbh-data.R
R/ath_aly_ncbi_dagchainer-data.R
R/ath_aly_ncbi_kaks-data.R
R/cds2genepos.R
R/cds2rbh.R
R/cdsdir2orthofinder.R
R/cdsfile2aafile.R
R/cdsfile2rbh.R
R/col2transparent.R
R/filter_alnlen.R
R/filter_eval.R
R/filter_pident.R
R/filter_qcov.R
R/filter_rost1999.R
R/filter_tcov.R
R/gff2longest.R
R/gtf2longest.R
R/hom_pan_ensembl_kaks-data.R
R/isoform2longest.R
R/make_dagchainer.R
R/make_last.R
R/make_vignette.R
R/plot_dagchainer.R
R/plot_kaks.R
R/rbh2dagchainer.R
R/rbh2kaks.R
R/seqid.R
R/tandemdups.R
README.md
_pkgdown.yml
data/aly.rda
data/ath.rda
data/ath_aly_crbh.rda
data/ath_aly_ncbi_dagchainer.rda
data/ath_aly_ncbi_kaks.rda
data/hom_pan_ensembl_kaks.rda
figure1.png
figure2.png
figure3.png
inst/CRBHitsLogo.png
inst/extdata/KaKs_Calculator2.0_src.tar.gz
inst/extdata/dagchainer.zip
inst/extdata/last-1542.zip
inst/fasta/aly.aa.fasta.gz
inst/fasta/aly.cds.fasta.gz
inst/fasta/ath.aa.fasta.gz
inst/fasta/ath.cds.fasta.gz
man/CRBHitsColors.Rd
man/aa2rbh.Rd
man/aadir2orthofinder.Rd
man/aafile2rbh.Rd
man/aly-data.Rd
man/ath-data.Rd
man/ath_aly_crbh-data.Rd
man/ath_aly_ncbi_dagchainer-data.Rd
man/ath_aly_ncbi_kaks-data.Rd
man/cds2genepos.Rd
man/cds2rbh.Rd
man/cdsdir2orthofinder.Rd
man/cdsfile2aafile.Rd
man/cdsfile2rbh.Rd
man/col2transparent.Rd
man/figures/figure1.png
man/figures/figure2.png
man/figures/figure3.png
man/figures/logo.png
man/filter_alnlen.Rd
man/filter_eval.Rd
man/filter_pident.Rd
man/filter_qcov.Rd
man/filter_rost1999.Rd
man/filter_tcov.Rd
man/gff2longest.Rd
man/gtf2longest.Rd
man/hom_pan_ensembl_kaks-data.Rd
man/isoform2longest.Rd
man/make_dagchainer.Rd
man/make_last.Rd
man/make_vignette.Rd
man/plot_dagchainer.Rd
man/plot_kaks.Rd
man/rbh2dagchainer.Rd
man/rbh2kaks.Rd
man/seqid.Rd
man/tandemdups.Rd
paper.bib
paper.md
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
public/404.html
public/CODE_OF_CONDUCT.html
public/LICENSE-text.html
public/apple-touch-icon-120x120.png
public/apple-touch-icon-152x152.png
public/apple-touch-icon-180x180.png
public/apple-touch-icon-60x60.png
public/apple-touch-icon-76x76.png
public/apple-touch-icon.png
public/articles/V01CRBHitsBasicVignette.html
public/articles/V01CRBHitsBasicVignette_files/accessible-code-block-0.0.1/empty-anchor.js
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-10-1.png
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-11-1.png
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-13-1.png
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-4-1.png
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-6-1.png
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-7-1.png
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-8-1.png
public/articles/V01CRBHitsBasicVignette_files/figure-html/unnamed-chunk-9-1.png
public/articles/V01CRBHitsBasicVignette_files/header-attrs-2.10/header-attrs.js
public/articles/V01CRBHitsBasicVignette_files/header-attrs-2.8/header-attrs.js
public/articles/V02-CRBHit-pairs-ARATHA-ARALYR.png
public/articles/V02-CRBHit-pairs-HOMSAP-PANTRO.png
public/articles/V02-CRBHit-pairs-selfblast-ARALYR.png
public/articles/V02-CRBHit-pairs-selfblast-ARATHA.png
public/articles/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-axis-size.png
public/articles/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-grid-axis-size.png
public/articles/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-grid-title-size.png
public/articles/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-title-size.png
public/articles/V02-dagchainer-default-ARATHA-ARALYR-selected-chr.png
public/articles/V02-dagchainer-default-ARATHA-ARALYR.png
public/articles/V02-dagchainer-default-HOMSAP-PANTRO-chr.png
public/articles/V02-dagchainer-inter-plus-intra-ARATHA-ARALYR-ignore-tandem.png
public/articles/V02-dagchainer-inter-plus-intra-ARATHA-ARALYR-only-tandem.png
public/articles/V02-dagchainer-inter-plus-intra-ARATHA-ARALYR-tandem.png
public/articles/V02-dagchainer-inter-plus-intra-HOMSAP-PANTRO-chr.png
public/articles/V02-dagchainer-selfblast-ARATHA-ignore-tandem.png
public/articles/V02-dagchainer-selfblast-ARATHA-only-tandem.png
public/articles/V02-dagchainer-selfblast-ARATHA-tandem.png
public/articles/V02-kaks-hist-HOMSAP-PANTRO.png
public/articles/V02-kaks-hist-chr-split.png
public/articles/V02-kaks-hist-chr.png
public/articles/V02-kaks-hist-min-max.png
public/articles/V02-kaks-hist.png
public/articles/V02-ks-hist.png
public/articles/V02-tandemdups-ARATHA.png
public/articles/V02-unnamed-chunk-10-1.png
public/articles/V02-unnamed-chunk-10-2.png
public/articles/V02-unnamed-chunk-10-3.png
public/articles/V02-unnamed-chunk-10-4.png
public/articles/V02-unnamed-chunk-10-5.png
public/articles/V02-unnamed-chunk-10-6.png
public/articles/V02-unnamed-chunk-11-1.png
public/articles/V02-unnamed-chunk-11-2.png
public/articles/V02-unnamed-chunk-11-3.png
public/articles/V02-unnamed-chunk-11-4.png
public/articles/V02-unnamed-chunk-12-1.png
public/articles/V02-unnamed-chunk-13-1.png
public/articles/V02-unnamed-chunk-13-2.png
public/articles/V02-unnamed-chunk-14-1.png
public/articles/V02-unnamed-chunk-4-1.png
public/articles/V02-unnamed-chunk-7-1.png
public/articles/V02-unnamed-chunk-7-2.png
public/articles/V02-unnamed-chunk-8-1.png
public/articles/V02KaKsVignette.html
public/articles/V02KaKsVignette_files/accessible-code-block-0.0.1/empty-anchor.js
public/articles/V02KaKsVignette_files/header-attrs-2.10/header-attrs.js
public/articles/V02KaKsVignette_files/header-attrs-2.8/header-attrs.js
public/articles/cds2rbh.png
public/articles/cds2rbhoverview.png
public/articles/index.html
public/articles/rbh2kaks.png
public/articles/rbh2kaksoverview.png
public/authors.html
public/bootstrap-toc.css
public/bootstrap-toc.js
public/docsearch.css
public/docsearch.js
public/favicon-16x16.png
public/favicon-32x32.png
public/favicon.ico
public/index.html
public/link.svg
public/logo.png
public/paper.html
public/pkgdown.css
public/pkgdown.js
public/pkgdown.yml
public/reference/CRBHitsColors-1.png
public/reference/CRBHitsColors-2.png
public/reference/CRBHitsColors.html
public/reference/GENETIC_CODE_TCAG.html
public/reference/Rplot001.png
public/reference/Rplot002.png
public/reference/Rplot003.png
public/reference/Rplot004.png
public/reference/aa2rbh-1.png
public/reference/aa2rbh-2.png
public/reference/aa2rbh.html
public/reference/aabin2aastring.html
public/reference/aadir2orthofinder.html
public/reference/aafile2rbh-1.png
public/reference/aafile2rbh-2.png
public/reference/aafile2rbh.html
public/reference/aastring2aabin.html
public/reference/aastring2aln.html
public/reference/aln2aastring.html
public/reference/aln2dnastring.html
public/reference/aly-data.html
public/reference/ath-data.html
public/reference/ath_aly_crbh-data.html
public/reference/ath_aly_ncbi_dagchainer-data.html
public/reference/ath_aly_ncbi_kaks-data.html
public/reference/cds2aa.html
public/reference/cds2codonaln.html
public/reference/cds2genepos.html
public/reference/cds2kaks.html
public/reference/cds2rbh-1.png
public/reference/cds2rbh-2.png
public/reference/cds2rbh.html
public/reference/cdsdir2orthofinder.html
public/reference/cdsfile2aafile.html
public/reference/cdsfile2rbh-1.png
public/reference/cdsfile2rbh-2.png
public/reference/cdsfile2rbh.html
public/reference/codon2numberAMBIG.html
public/reference/codon2numberTCAG.html
public/reference/codonmat2pnps.html
public/reference/codonmat2xy.html
public/reference/col2transparent-1.png
public/reference/col2transparent-2.png
public/reference/col2transparent-3.png
public/reference/col2transparent-4.png
public/reference/col2transparent.html
public/reference/compareCodons.html
public/reference/dnabin2dnastring.html
public/reference/dnastring2aln.html
public/reference/dnastring2codonmat.html
public/reference/dnastring2dnabin.html
public/reference/dnastring2kaks.html
public/reference/figures/figure1.png
public/reference/figures/figure2.png
public/reference/figures/figure3.png
public/reference/figures/logo.png
public/reference/filter_alnlen.html
public/reference/filter_eval.html
public/reference/filter_pident.html
public/reference/filter_qcov.html
public/reference/filter_rost1999.html
public/reference/filter_tcov.html
public/reference/gff2longest.html
public/reference/globalDeletion.html
public/reference/gtf2longest.html
public/reference/hiv-data.html
public/reference/hom_pan_ensembl_kaks-data.html
public/reference/index.html
public/reference/isoform2longest.html
public/reference/makePostalignedSeqs.html
public/reference/make_KaKs_Calculator2.html
public/reference/make_dagchainer.html
public/reference/make_last.html
public/reference/make_vignette.html
public/reference/plot_dagchainer-1.png
public/reference/plot_dagchainer-2.png
public/reference/plot_dagchainer.html
public/reference/plot_kaks-1.png
public/reference/plot_kaks-2.png
public/reference/plot_kaks.html
public/reference/rbh2dagchainer-1.png
public/reference/rbh2dagchainer-2.png
public/reference/rbh2dagchainer.html
public/reference/rbh2kaks-1.png
public/reference/rbh2kaks.html
public/reference/seqid.html
public/reference/subString.html
public/reference/tandemdups-1.png
public/reference/tandemdups.html
public/reference/uptriidx.html
public/sitemap.xml
tests/testthat.R
tests/testthat/test-cds2rbh.R
tests/testthat/test-cdsfile2aafile.R
tests/testthat/test-cdsfile2rbh.R
tests/testthat/test-filterRost1999.R
tests/testthat/test-rbh2kaks.R
vignettes/V01CRBHitsBasicVignette.R
vignettes/V01CRBHitsBasicVignette.Rmd
vignettes/V01CRBHitsBasicVignette.html
vignettes/V02-CRBHit-pairs-ARATHA-ARALYR.png
vignettes/V02-CRBHit-pairs-HOMSAP-PANTRO.png
vignettes/V02-CRBHit-pairs-selfblast-ARALYR.png
vignettes/V02-CRBHit-pairs-selfblast-ARATHA.png
vignettes/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-axis-size.png
vignettes/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-grid-axis-size.png
vignettes/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-grid-title-size.png
vignettes/V02-dagchainer-default-ARATHA-ARALYR-selected-chr-title-size.png
vignettes/V02-dagchainer-default-ARATHA-ARALYR-selected-chr.png
vignettes/V02-dagchainer-default-ARATHA-ARALYR.png
vignettes/V02-dagchainer-default-HOMSAP-PANTRO-chr.png
vignettes/V02-dagchainer-inter-plus-intra-ARATHA-ARALYR-ignore-tandem.png
vignettes/V02-dagchainer-inter-plus-intra-ARATHA-ARALYR-only-tandem.png
vignettes/V02-dagchainer-inter-plus-intra-ARATHA-ARALYR-tandem.png
vignettes/V02-dagchainer-inter-plus-intra-HOMSAP-PANTRO-chr.png
vignettes/V02-dagchainer-selfblast-ARATHA-ignore-tandem.png
vignettes/V02-dagchainer-selfblast-ARATHA-only-tandem.png
vignettes/V02-dagchainer-selfblast-ARATHA-tandem.png
vignettes/V02-kaks-hist-HOMSAP-PANTRO.png
vignettes/V02-kaks-hist-chr-split.png
vignettes/V02-kaks-hist-chr.png
vignettes/V02-kaks-hist-min-max.png
vignettes/V02-kaks-hist.png
vignettes/V02-ks-hist.png
vignettes/V02-tandemdups-ARATHA.png
vignettes/V02KaKsVignette.R
vignettes/V02KaKsVignette.Rmd
vignettes/V02KaKsVignette.html
vignettes/cds2rbh.png
vignettes/cds2rbhoverview.png
vignettes/rbh2kaks.png
vignettes/rbh2kaksoverview.png
