Files in arendsee/fagin
Annotate Orphan Genes
.Rbuildignore
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
FUNDING
LICENSE
NAMESPACE
NEWS.md
R/analysis_1.R
R/analysis_2.R
R/analysis_3.R
R/analysis_4.R
R/class.R
R/class_accessors.R
R/class_print.R
R/class_summarize.R
R/cosmetics_warnings.R
R/data.R
R/exploration.R
R/fagin.R
R/functions_alignments.R
R/functions_derive.R
R/functions_indels.R
R/functions_overlaps.R
R/gene-pages.R
R/gff_handling.R
R/types.R
R/util_cache.R
R/util_load.R
R/util_misc.R
R/yeast_config.R
R/z_nucleotide.R
R/z_protein.R
R/z_tree.R
README.md
codecov.yml
inst/misc/misc/README
inst/misc/misc/blastp-vs-others.sh
inst/misc/misc/build-pbs.sh
inst/misc/misc/max-hit.sh
inst/misc/misc/mid-process.sh
inst/misc/misc/orphans-analysis.sh
inst/misc/misc/retrieve-brassicaceae-test-data.sh
inst/misc/misc/retrieve-drosophila-test-data.sh
inst/misc/misc/satsuma.pbs
inst/misc/misc/search-gff.py
inst/misc/tandem-repeat-analysis/parse-treks-output.pl
inst/misc/tandem-repeat-analysis/sample-input/outfile
inst/tiny/test.fna
inst/tiny/test.gff
inst/tiny/tiny.tree
inst/tiny/unicorn-genelist.txt
inst/tiny/unicorn.vs.centaur.syn
inst/yeast/control-list.txt
inst/yeast/fna/Saccharomyces_arboricola.fna
inst/yeast/fna/Saccharomyces_cerevisiae.fna
inst/yeast/fna/Saccharomyces_eubayanus.fna
inst/yeast/fna/Saccharomyces_kudriavzevii.fna
inst/yeast/fna/Saccharomyces_mikatae.fna
inst/yeast/fna/Saccharomyces_paradoxus.fna
inst/yeast/fna/Saccharomyces_uvarum.fna
inst/yeast/gff/Saccharomyces_arboricola.gff
inst/yeast/gff/Saccharomyces_cerevisiae.gff
inst/yeast/gff/Saccharomyces_eubayanus.gff
inst/yeast/gff/Saccharomyces_kudriavzevii.gff
inst/yeast/gff/Saccharomyces_mikatae.gff
inst/yeast/gff/Saccharomyces_paradoxus.gff
inst/yeast/gff/Saccharomyces_uvarum.gff
inst/yeast/orphan-list.txt
inst/yeast/phylostratr-species.Rds
inst/yeast/phylostratr-strata.Rds
inst/yeast/smalltree
inst/yeast/syn/Saccharomyces_cerevisiae.vs.Saccharomyces_arboricola.syn
inst/yeast/syn/Saccharomyces_cerevisiae.vs.Saccharomyces_eubayanus.syn
inst/yeast/syn/Saccharomyces_cerevisiae.vs.Saccharomyces_kudriavzevii.syn
inst/yeast/syn/Saccharomyces_cerevisiae.vs.Saccharomyces_mikatae.syn
inst/yeast/syn/Saccharomyces_cerevisiae.vs.Saccharomyces_paradoxus.syn
inst/yeast/syn/Saccharomyces_cerevisiae.vs.Saccharomyces_uvarum.syn
inst/yeast/test-faa/id2name.tsv
inst/yeast/tree
man/config.Rd
man/config_alignment-class.Rd
man/config_alignment_simulation-class.Rd
man/config_alignment_thresholds-class.Rd
man/config_input-class.Rd
man/config_orf-class.Rd
man/config_synder-class.Rd
man/derive_genomic_ORFs.Rd
man/derive_nstring.Rd
man/derive_transcript_ORFs.Rd
man/derived_input-class.Rd
man/determine_labels.Rd
man/determine_origins.Rd
man/dgumbel.Rd
man/dna_summary-class.Rd
man/dnaregex.Rd
man/extract_with_complements.Rd
man/faa_summary-class.Rd
man/fagin.Rd
man/fagin_config-class.Rd
man/fagin_io.Rd
man/fagin_printer.Rd
man/fagin_summary.Rd
man/final_protein_residue_counts.Rd
man/genomic_composition.Rd
man/get_species.Rd
man/get_species_phylogenetic_order.Rd
man/get_summaries.Rd
man/get_synder_count_table.Rd
man/get_synder_nsi.Rd
man/get_targets.Rd
man/gff_summary-class.Rd
man/granges_summary-class.Rd
man/initial_protein_residue_counts.Rd
man/load_gene_models.Rd
man/make_excel_spreadsheet.Rd
man/make_fagin_cacher.Rd
man/make_format_translation_warning.Rd
man/make_genome_table.Rd
man/make_origin_table.Rd
man/make_query_target_table.Rd
man/make_result_archive.Rd
man/make_secondary_genewise_table.Rd
man/make_secondary_labels_table.Rd
man/make_synder_flag_table.Rd
man/make_synder_table.Rd
man/make_synmap_table.Rd
man/merge_named_vectors.Rd
man/number_of_scaffolds.Rd
man/numeric_summary-class.Rd
man/pgumbel.Rd
man/phase_summary-class.Rd
man/plot_secondary_labels.Rd
man/primary_data.Rd
man/protein_has_internal_stop.Rd
man/qgumbel.Rd
man/run_fagin.Rd
man/secondary_data.Rd
man/seq_summary-class.Rd
man/species_data_files-class.Rd
man/species_meta-class.Rd
man/species_summaries-class.Rd
man/synmap_summary-class.Rd
man/synteny_meta-class.Rd
man/tertiary_data.Rd
man/validate_config.Rd
man/yeast_config.Rd
tests/testthat.R
tests/testthat/test-DNAStringSet.R
tests/testthat/test-FaFile.R
tests/testthat/test-TxDb.R
tests/testthat/test-extract.R
tests/testthat/test-filenaming.R
tests/testthat/test-large.R
tests/testthat/test-reading.R
tests/testthat/test-unplaced.R
