Files in ropensci/phylotaR
Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

.Rbuildignore
.github/CONTRIBUTING.md .github/issue_template.md .github/pull_request_template.md
.gitignore
.travis.yml
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/all-classes.R R/phylotaR.R R/pipeline-tools.R R/pipeline.R R/stage1-tools.R R/stage1.R R/stage2-tools.R R/stage2.R R/stage3-tools.R R/stage3.R R/stage4-tools.R R/stage4.R R/tools-api.R R/tools-blast.R R/tools-cache.R R/tools-entrez.R R/tools-log.R R/tools-sqs.R R/tools-system.R R/tools-tests.R R/tools-txdct.R R/user-calc.R R/user-drop.R R/user-get.R R/user-special.R README.md
_pkgdown.yml
codemeta.json
data/aotus.rda
data/bromeliads.rda
data/cycads.rda
data/dragonflies.rda
data/sturgeons.rda
data/tardigrades.rda
data/tinamous.rda
data/yeasts.rda
demos/demo_run.R
docs/CONTRIBUTING.html
docs/LICENSE-text.html
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docs/apple-touch-icon.png
docs/articles/index.html
docs/articles/phylotaR-advanced.html
docs/articles/phylotaR.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
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docs/favicon.ico
docs/index.html
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docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/pull_request_template.html
docs/reference/ClstrArc-class.html
docs/reference/ClstrRec-class.html
docs/reference/Phylota-class.html
docs/reference/SeqArc-class.html
docs/reference/SeqRec-class.html
docs/reference/TaxDict-class.html
docs/reference/TaxRec-class.html
docs/reference/aotus.rd
docs/reference/batcher.html
docs/reference/blast_clstr.html
docs/reference/blast_filter.html
docs/reference/blast_setup.html
docs/reference/blast_sqs.html
docs/reference/blastcache_load.html
docs/reference/blastcache_save.html
docs/reference/blastdb_gen.html
docs/reference/blastn_run.html
docs/reference/blst_rs.html
docs/reference/bromeliads.rd
docs/reference/cache_rm.html
docs/reference/cache_setup.html
docs/reference/calc_mad.html
docs/reference/calc_wrdfrq.html
docs/reference/clade_select.html
docs/reference/clstr2_calc.html
docs/reference/clstr_all.html
docs/reference/clstr_direct.html
docs/reference/clstr_sqs.html
docs/reference/clstr_subtree.html
docs/reference/clstrarc_gen.html
docs/reference/clstrarc_join.html
docs/reference/clstrrec_gen.html
docs/reference/clstrs_calc.html
docs/reference/clstrs_join.html
docs/reference/clstrs_merge.html
docs/reference/clstrs_renumber.html
docs/reference/clstrs_save.html
docs/reference/clusters2_run.html
docs/reference/clusters_run.html
docs/reference/cmdln.html
docs/reference/cycads.rd
docs/reference/descendants_get.html
docs/reference/download_obj_check.html
docs/reference/download_run.html
docs/reference/dragonflies.rd
docs/reference/drop_by_rank.html
docs/reference/drop_cls.html
docs/reference/drop_clstrs.html
docs/reference/drop_sqs.html
docs/reference/error.html
docs/reference/gb_extract.html
docs/reference/get_clstr_slot.html
docs/reference/get_nsqs.html
docs/reference/get_ntaxa.html
docs/reference/get_sq_slot.html
docs/reference/get_stage_times.html
docs/reference/get_tx_slot.html
docs/reference/get_txids.html
docs/reference/hierarchic_download.html
docs/reference/index.html
docs/reference/info.html
docs/reference/is_txid_in_clstr.html
docs/reference/is_txid_in_sq.html
docs/reference/list_clstrrec_slots.html
docs/reference/list_ncbi_ranks.html
docs/reference/list_seqrec_slots.html
docs/reference/list_taxrec_slots.html
docs/reference/mk_txid_in_sq_mtrx.html
docs/reference/ncbicache_load.html
docs/reference/ncbicache_save.html
docs/reference/obj_check.html
docs/reference/obj_load.html
docs/reference/obj_save.html
docs/reference/parameters.html
docs/reference/parameters_load.html
docs/reference/parameters_reset.html
docs/reference/parameters_setup.html
docs/reference/parent_get.html
docs/reference/plot_phylota_pa-1.png
docs/reference/plot_phylota_pa-2.png
docs/reference/plot_phylota_pa.html
docs/reference/plot_phylota_treemap-1.png
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docs/reference/plot_phylota_treemap.html
docs/reference/progress_init.html
docs/reference/progress_read.html
docs/reference/progress_reset.html
docs/reference/progress_save.html
docs/reference/rank_get.html
docs/reference/rawseqrec_breakdown.html
docs/reference/read_phylota.html
docs/reference/reset.html
docs/reference/restart.html
docs/reference/run.html
docs/reference/safely_connect.html
docs/reference/search_and_cache.html
docs/reference/searchterm_gen.html
docs/reference/seeds_blast.html
docs/reference/seq_download.html
docs/reference/seqarc_gen.html
docs/reference/seqrec_augment.html
docs/reference/seqrec_convert.html
docs/reference/seqrec_gen.html
docs/reference/seqrec_get.html
docs/reference/setup.html
docs/reference/sids_check.html
docs/reference/sids_get.html
docs/reference/sids_load.html
docs/reference/sids_save.html
docs/reference/sqs_count.html
docs/reference/sqs_load.html
docs/reference/sqs_save.html
docs/reference/stage_args_check.html
docs/reference/stages_run.html
docs/reference/sturgeons.rd
docs/reference/summary_phylota.html
docs/reference/tardigrades.rd
docs/reference/tax_download.html
docs/reference/taxdict_gen.html
docs/reference/taxise_run.html
docs/reference/taxtree_gen.html
docs/reference/tinamous.rd
docs/reference/txids_get.html
docs/reference/txnds_count.html
docs/reference/update_phylota.html
docs/reference/warn.html
docs/reference/write_phylota.html
docs/reference/write_sqs.html
docs/reference/yeasts.rd examples/calc_mad.R examples/calc_wrdfrq.R examples/clstrarc-class.R examples/clstrrec-class.R examples/clusters2_run.R examples/clusters_run.R examples/download_run.R examples/drop_by_rank.R examples/drop_clstrs.R examples/drop_sqs.R examples/get_clstr_slot.R examples/get_nsqs.R examples/get_ntaxa.R examples/get_sq_slot.R examples/get_stage_times.R examples/get_tx_slot.R examples/get_txids.R examples/is_txid_in_clstr.R examples/is_txid_in_sq.R examples/parameters_reset.R examples/phylota-class.R examples/plot_phylota_pa.R examples/plot_phylota_treemap.R examples/read_phylota.R examples/reset.R examples/restart.R examples/run.R examples/seqarc-class.R examples/seqrec-class.R examples/setup.R examples/taxdict-class.R examples/taxise_run.R examples/taxrec-class.R examples/write_sqs.R
logo.png
man-roxygen/lvl.R man-roxygen/ps.R man/ClstrArc-class.Rd man/ClstrRec-class.Rd man/Phylota-class.Rd man/SeqArc-class.Rd man/SeqRec-class.Rd man/TaxDict-class.Rd man/TaxRec-class.Rd man/aotus.rd man/batcher.Rd man/blast_clstr.Rd man/blast_filter.Rd man/blast_setup.Rd man/blast_sqs.Rd man/blastcache_load.Rd man/blastcache_save.Rd man/blastdb_gen.Rd man/blastn_run.Rd man/bromeliads.rd man/cache_rm.Rd man/cache_setup.Rd man/calc_mad.Rd man/calc_wrdfrq.Rd man/clade_select.Rd man/clstr2_calc.Rd man/clstr_all.Rd man/clstr_direct.Rd man/clstr_sqs.Rd man/clstr_subtree.Rd man/clstrarc_gen.Rd man/clstrarc_join.Rd man/clstrrec_gen.Rd man/clstrs_calc.Rd man/clstrs_join.Rd man/clstrs_merge.Rd man/clstrs_renumber.Rd man/clstrs_save.Rd man/clusters2_run.Rd man/clusters_run.Rd man/cmdln.Rd man/cycads.rd man/descendants_get.Rd man/download_obj_check.Rd man/download_run.Rd man/dragonflies.rd man/drop_by_rank.Rd man/drop_clstrs.Rd man/drop_sqs.Rd man/error.Rd man/gb_extract.Rd man/get_clstr_slot.Rd man/get_nsqs.Rd man/get_ntaxa.Rd man/get_sq_slot.Rd man/get_stage_times.Rd man/get_tx_slot.Rd man/get_txids.Rd man/hierarchic_download.Rd man/info.Rd man/is_txid_in_clstr.Rd man/is_txid_in_sq.Rd man/list_clstrrec_slots.Rd man/list_ncbi_ranks.Rd man/list_seqrec_slots.Rd man/list_taxrec_slots.Rd man/mk_txid_in_sq_mtrx.Rd man/ncbicache_load.Rd man/ncbicache_save.Rd man/obj_check.Rd man/obj_load.Rd man/obj_save.Rd man/outfmt_get.Rd man/parameters.Rd man/parameters_load.Rd man/parameters_reset.Rd man/parameters_setup.Rd man/parent_get.Rd man/plot_phylota_pa.Rd man/plot_phylota_treemap.Rd man/progress_init.Rd man/progress_read.Rd man/progress_reset.Rd man/progress_save.Rd man/rank_get.Rd man/rawseqrec_breakdown.Rd man/read_phylota.Rd man/reset.Rd man/restart.Rd man/run.Rd man/safely_connect.Rd man/search_and_cache.Rd man/searchterm_gen.Rd man/seeds_blast.Rd man/seq_download.Rd man/seqarc_gen.Rd man/seqrec_augment.Rd man/seqrec_convert.Rd man/seqrec_gen.Rd man/seqrec_get.Rd man/setup.Rd man/sids_check.Rd man/sids_get.Rd man/sids_load.Rd man/sids_save.Rd man/sqs_count.Rd man/sqs_save.Rd man/stage_args_check.Rd man/stages_run.Rd man/sturgeons.rd man/summary_phylota.Rd man/tardigrades.rd man/tax_download.Rd man/taxdict_gen.Rd man/taxise_run.Rd man/taxtree_gen.Rd man/tinamous.rd man/txids_get.Rd man/txnds_count.Rd man/update_phylota.Rd man/warn.Rd man/write_sqs.Rd man/yeasts.rd other/aedes_culex.R other/dev.R other/make_phylota_data.R other/make_taxonomy_test_data.R other/spell_check.R
other/stages.png
other/unused.R
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pkgdown/favicon/favicon.ico
tests/test-all.R
tests/testthat/data/api/entrez_fetch_seqs.rda
tests/testthat/data/api/entrez_fetch_sid.rda
tests/testthat/data/api/entrez_search_sid.rda
tests/testthat/data/api/entrez_search_tax.rda
tests/testthat/data/api/xml_timeout.rda
tests/testthat/data/blast/README
tests/testthat/data/blast/blast_res.rda
tests/testthat/data/blast/testblstn
tests/testthat/data/blast/testdb.nhr
tests/testthat/data/blast/testdb.nin
tests/testthat/data/blast/testdb.nsq
tests/testthat/data/clstrarc.rda
tests/testthat/data/raw_seqrecs.rda
tests/testthat/data/raw_txrecs.rda
tests/testthat/data/sqrecs.rda
tests/testthat/data/taxonomy/txids_records.RData
tests/testthat/data/test_raw_seqrecs.rda
tests/testthat/data/txdct.rda
tests/testthat/data/txrecs.rda
tests/testthat/test-all-class.R tests/testthat/test-phylotar.R tests/testthat/test-pipeline.R tests/testthat/test-stage1-tools.R tests/testthat/test-stage1.R tests/testthat/test-stage2-tools.R tests/testthat/test-stage2.R tests/testthat/test-stage3-tools.R tests/testthat/test-stage3.R tests/testthat/test-stage4-tools.R tests/testthat/test-stage4.R tests/testthat/test-tools-api.R tests/testthat/test-tools-blast.R tests/testthat/test-tools-cache.R tests/testthat/test-tools-entrez.R tests/testthat/test-tools-log.R tests/testthat/test-tools-pipeline.R tests/testthat/test-tools-sqs.R tests/testthat/test-tools-system.R tests/testthat/test-tools-test.R tests/testthat/test-tools-txdct.R tests/testthat/test-user-calc.R tests/testthat/test-user-drop.R tests/testthat/test-user-get.R tests/testthat/test-user-special.R vignettes/phylotaR.R vignettes/phylotaR.Rmd
vignettes/phylotaR.html
ropensci/phylotaR documentation built on Jan. 16, 2020, 11:47 a.m.