kullrich/CRBHits
Conditional reciprocal best hits (CRBHits) in R

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kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R
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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/aafile2rbhplus.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-1595.zip
inst/extdata/maf-convert-crbhits
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/aafile2rbhplus.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/figures/searchtool_comparison_venn.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/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
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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/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/V02KaKsVignette.html
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/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
public/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
public/deps/bootstrap-5.3.1/bootstrap.min.css
public/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
public/deps/clipboard.js-2.0.11/clipboard.min.js
public/deps/data-deps.txt
public/deps/font-awesome-6.4.2/css/all.css
public/deps/font-awesome-6.4.2/css/all.min.css
public/deps/font-awesome-6.4.2/css/v4-shims.css
public/deps/font-awesome-6.4.2/css/v4-shims.min.css
public/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
public/deps/font-awesome-6.4.2/webfonts/fa-brands-400.woff2
public/deps/font-awesome-6.4.2/webfonts/fa-regular-400.ttf
public/deps/font-awesome-6.4.2/webfonts/fa-regular-400.woff2
public/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
public/deps/font-awesome-6.4.2/webfonts/fa-solid-900.woff2
public/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
public/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
public/deps/headroom-0.11.0/headroom.min.js
public/deps/headroom-0.11.0/jQuery.headroom.min.js
public/deps/jquery-3.6.0/jquery-3.6.0.js
public/deps/jquery-3.6.0/jquery-3.6.0.min.js
public/deps/jquery-3.6.0/jquery-3.6.0.min.map
public/deps/search-1.0.0/autocomplete.jquery.min.js
public/deps/search-1.0.0/fuse.min.js
public/deps/search-1.0.0/mark.min.js
public/docsearch.css
public/docsearch.js
public/favicon-16x16.png
public/favicon-32x32.png
public/favicon.ico
public/index.html
public/katex-auto.js
public/lightswitch.js
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/aa2rbh-1.png
public/reference/aa2rbh-2.png
public/reference/aa2rbh.html
public/reference/aadir2orthofinder.html
public/reference/aafile2rbh-1.png
public/reference/aafile2rbh-2.png
public/reference/aafile2rbh.html
public/reference/aafile2rbhplus-1.png
public/reference/aafile2rbhplus-2.png
public/reference/aafile2rbhplus.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/cds2genepos.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/col2transparent-1.png
public/reference/col2transparent-2.png
public/reference/col2transparent-3.png
public/reference/col2transparent-4.png
public/reference/col2transparent.html
public/reference/figures/figure1.png
public/reference/figures/figure2.png
public/reference/figures/figure3.png
public/reference/figures/logo.png
public/reference/figures/searchtool_comparison_venn.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/gtf2longest.html
public/reference/hom_pan_ensembl_kaks-data.html
public/reference/index.html
public/reference/isoform2longest.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/tandemdups-1.png
public/reference/tandemdups.html
public/search.json
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
kullrich/CRBHits documentation built on Nov. 13, 2024, 7:44 a.m.

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