Files in joelnitta/baitfindR
Find Baits for Sequence Capture
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/bedtools.R
R/blast.R
R/calculate_alignment_stats.R
R/data.R
R/etc.R
R/fill_introns.R
R/filter_fasta.R
R/mcl.R
R/t_coffee.R
R/transdecoder.R
R/utils-pipe.R
R/yang_and_smith.R
README.md
_pkgdown.yaml
baitfindR.Rproj
data-raw/get_proteomes.R
data-raw/make_small_arabi_genome.Rmd
data-raw/make_small_arabi_genome.md
data-raw/make_small_arabi_gff.Rmd
data-raw/make_small_arabi_gff.md
data-raw/make_small_transcriptome.Rmd
data-raw/make_small_transcriptome.md
data-raw/trim_transcriptomes.R
data/example_transcriptomes.rda
data/onekp_data.rda
docker-compose.yml
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/_config.yml
docs/articles/index.html
docs/articles/translation.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/blast_n.html
docs/reference/blast_n_list.html
docs/reference/blast_p.html
docs/reference/blast_to_mcl.html
docs/reference/build_blast_db.html
docs/reference/calculate_alignment_stats.html
docs/reference/cat_files.html
docs/reference/cd_hit_est.html
docs/reference/clean_gff.html
docs/reference/cut_long_internal_branches.html
docs/reference/delete_old_output.html
docs/reference/example_transcriptomes.html
docs/reference/extract_blast_hits.html
docs/reference/extract_regions_from_fasta.html
docs/reference/fasta_to_tree.html
docs/reference/fill_introns-1.png
docs/reference/fill_introns-2.png
docs/reference/fill_introns.html
docs/reference/filter_1to1_orthologs.html
docs/reference/filter_fasta.html
docs/reference/find_bed_regions.html
docs/reference/fix_names_from_transdecoder.html
docs/reference/get_out_hash.html
docs/reference/index.html
docs/reference/mafft_wrapper.html
docs/reference/make_dir.html
docs/reference/mask_regions_in_fasta.html
docs/reference/mask_tips_by_taxonID_transcripts.html
docs/reference/mcl.html
docs/reference/onekp_data.html
docs/reference/phyutility_wrapper.html
docs/reference/pipe.html
docs/reference/prune_paralogs_MI.html
docs/reference/prune_paralogs_MO.html
docs/reference/prune_paralogs_RT.html
docs/reference/realign_with_best_hits.html
docs/reference/set_ys_path.html
docs/reference/tcs.html
docs/reference/tcs_loop.html
docs/reference/transdecoder_long_orfs.html
docs/reference/transdecoder_predict.html
docs/reference/trim_both_ends.html
docs/reference/trim_one_end.html
docs/reference/trim_tips.html
docs/reference/write_fasta_files.html
docs/reference/write_fasta_files_from_mcl.html
docs/reference/write_fasta_files_from_trees.html
docs/reference/write_ortholog_fasta_files.html
docs/sitemap.xml
inst/extdata/Arabidopsis_thaliana_TAIR10_40_small.fasta
inst/extdata/Arabidopsis_thaliana_TAIR10_40_small.gff3
man/blast_n.Rd
man/blast_n_list.Rd
man/blast_p.Rd
man/blast_to_mcl.Rd
man/build_blast_db.Rd
man/calculate_alignment_stats.Rd
man/cat_files.Rd
man/cd_hit_est.Rd
man/clean_gff.Rd
man/cut_long_internal_branches.Rd
man/delete_old_output.Rd
man/example_transcriptomes.Rd
man/extract_blast_hits.Rd
man/extract_regions_from_fasta.Rd
man/fasta_to_tree.Rd
man/fill_introns.Rd
man/filter_1to1_orthologs.Rd
man/filter_fasta.Rd
man/find_bed_regions.Rd
man/fix_names_from_transdecoder.Rd
man/get_out_hash.Rd
man/mafft_wrapper.Rd
man/make_dir.Rd
man/mask_regions_in_fasta.Rd
man/mask_tips_by_taxonID_transcripts.Rd
man/mcl.Rd
man/onekp_data.Rd
man/phyutility_wrapper.Rd
man/pipe.Rd
man/prune_paralogs_MI.Rd
man/prune_paralogs_MO.Rd
man/prune_paralogs_RT.Rd
man/realign_with_best_hits.Rd
man/set_ys_path.Rd
man/tcs.Rd
man/tcs_loop.Rd
man/transdecoder_long_orfs.Rd
man/transdecoder_predict.Rd
man/trim_both_ends.Rd
man/trim_one_end.Rd
man/trim_tips.Rd
man/write_fasta_files.Rd
man/write_fasta_files_from_mcl.Rd
man/write_fasta_files_from_trees.Rd
man/write_ortholog_fasta_files.Rd
vignettes/.gitignore
vignettes/translation.Rmd
