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

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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

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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

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public/articles/V02-dagchainer-default-ARATHA-ARALYR.png

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public/articles/V02-dagchainer-inter-plus-intra-ARATHA-ARALYR-ignore-tandem.png

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public/articles/V02-dagchainer-selfblast-ARATHA-ignore-tandem.png

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public/articles/V02-kaks-hist-HOMSAP-PANTRO.png

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public/articles/V02-kaks-hist.png

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public/pkgdown.js

public/pkgdown.yml

public/reference/CRBHitsColors-1.png

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public/reference/CRBHitsColors.html

public/reference/GENETIC_CODE_TCAG.html

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public/reference/aastring2aabin.html

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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

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public/reference/cds2rbh.html

public/reference/cdsdir2orthofinder.html

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public/reference/cdsfile2rbh.html

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public/reference/compareCodons.html

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public/reference/dnastring2aln.html

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public/reference/dnastring2dnabin.html

public/reference/dnastring2kaks.html

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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

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public/reference/make_vignette.html

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public/reference/seqid.html

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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 March 29, 2024, 11:34 a.m.

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

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

R Package Documentation

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

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

R Package Documentation

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

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