Files in almeidasilvaf/cogeqc
Systematic quality checks on comparative genomics analyses
.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/ISSUE_TEMPLATE/issue_template.md
.github/SUPPORT.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/cogeqc-package.R
R/data.R
R/file_import.R
R/genome_assembly.R
R/homology_detection.R
R/synteny.R
R/utils.R
R/visualization.R
README.Rmd
README.md
codecov.yml
data/batch_summary.rda
data/interpro_ath.rda
data/interpro_bol.rda
data/og.rda
data/synnet.rda
data/tree.rda
dev/01_create_pkg.R
dev/02_git_github_setup.R
dev/03_core_files.R
dev/04_update.R
inst/CITATION
inst/_pkgdown.yml
inst/extdata/Duplications_per_Species_Tree_Node.tsv
inst/extdata/Hse_subset.fa
inst/extdata/Orthogroups.tsv.gz
inst/extdata/Orthogroups_SpeciesOverlaps.tsv
inst/extdata/Statistics_PerSpecies.tsv
inst/extdata/short_summary.txt
inst/script/data_creation.md
man/assess_orthogroups.Rd
man/assess_synnet.Rd
man/assess_synnet_list.Rd
man/batch_summary.Rd
man/busco_is_installed.Rd
man/calculate_H.Rd
man/cogeqc-package.Rd
man/compare_genome_stats.Rd
man/compare_orthogroups.Rd
man/figures/logo.png
man/fit_sft.Rd
man/get_genome_stats.Rd
man/interpro_ath.Rd
man/interpro_bol.Rd
man/list_busco_datasets.Rd
man/og.Rd
man/plot_busco.Rd
man/plot_duplications.Rd
man/plot_genes_in_ogs.Rd
man/plot_genome_stats.Rd
man/plot_og_overlap.Rd
man/plot_og_sizes.Rd
man/plot_orthofinder_stats.Rd
man/plot_species_specific_ogs.Rd
man/plot_species_tree.Rd
man/read_busco.Rd
man/read_orthofinder_stats.Rd
man/read_orthogroups.Rd
man/run_busco.Rd
man/synnet.Rd
man/tree.Rd
tests/testthat.R
tests/testthat/test-file_import.R
tests/testthat/test-genome_assembly.R
tests/testthat/test-homology_detection.R
tests/testthat/test-synteny.R
tests/testthat/test-utils.R
tests/testthat/test-visualization.R
vignettes/.gitignore
vignettes/vignette_01.bib
vignettes/vignette_01_assessing_genome_assembly.Rmd
vignettes/vignette_02.bib
vignettes/vignette_02_assessing_orthogroup_inference.Rmd
vignettes/vignette_03.bib
vignettes/vignette_03_assessing_synteny.Rmd
