Files in arendsee/phylostratr
Analyze phylostratigraphic data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/analysis.R
R/blast.R
R/check.R
R/class.R
R/counts.R
R/data.R
R/diagnostics.R
R/generics.R
R/hmmer.R
R/io.R
R/ncbi-taxonomy.R
R/phylostratr.R
R/plot.R
R/reports.R
R/sequence.R
R/strata.R
R/tree_building.R
R/tree_manipulation.R
R/uniprot-access.R
R/util.R
README-fig1.png
README.md
codecov.yml
data/arabidopsis.rda
data/arabidopsis_strata.rda
data/atree.rda
data/saccharomyces.rda
inst/CITATION
inst/case-studies/arabidopsis-supplemental.Rmd
inst/case-studies/figure/fig_heatmap.eps
inst/case-studies/figure/fig_heatmap.png
inst/case-studies/tips-ages.tab
inst/case-studies/yeast-supplemental.Rmd
inst/extdata/arendsee2014_strata.tab
inst/extdata/carvunis2012_strata.tab
inst/extdata/prokaryote_sample.rda
inst/extdata/yeast/tree
inst/sparql/get-all-mitochondrial-uniprot-ids.rq
inst/sparql/get-all-taxid-sequences.rq
inst/sparql/get-representative-proteome-pfam-map.rq
inst/sparql/get-representative-proteome-sequences.rq
inst/sparql/get-representative-proteome-sizes.rq
inst/sparql/get-representative-proteome-taxids.rq
man/CountMatrix.Rd
man/Strata.Rd
man/add_organelle_proteins.Rd
man/add_proteome_stats.Rd
man/add_taxa.Rd
man/arabidopsis.Rd
man/arabidopsis_strata.Rd
man/atree.Rd
man/children.Rd
man/classify_by_adjusted_pvalue.Rd
man/classify_by_evalue.Rd
man/classify_by_pvalue.Rd
man/clean_phyid.Rd
man/constrict.Rd
man/data_tree_to_result_tree.Rd
man/descendent_nodes.Rd
man/descendents.Rd
man/diverse_subtree.Rd
man/edgelist_to_phylo.Rd
man/extract_uniprot_id_from_fasta.Rd
man/find_revenants.Rd
man/get_besthit.Rd
man/get_max_hit.Rd
man/get_mrca_names.Rd
man/get_phylostrata_map.Rd
man/get_root.Rd
man/has_header.Rd
man/homolog_tree_to_phylostrata.Rd
man/is_root.Rd
man/is_valid_strata.Rd
man/leafs.Rd
man/lineage.Rd
man/lineage_to_ancestor_tree.Rd
man/lineages_to_phylo.Rd
man/load_hittable.Rd
man/make_blast_database.Rd
man/make_diamond_database.Rd
man/make_jump_matrix.Rd
man/make_matrix_from_two_strata.Rd
man/make_significance_matrices.Rd
man/make_tree_relative_to.Rd
man/map_ids.Rd
man/map_node_label.Rd
man/merge_besthits.Rd
man/merge_phylo.Rd
man/ncbi_ancestors.Rd
man/ncbi_aunts.Rd
man/ncbi_cousins.Rd
man/ncbi_tree.Rd
man/nleafs.Rd
man/nodes.Rd
man/normalize_matrix_by_col.Rd
man/normalize_matrix_by_row.Rd
man/organelle_table.Rd
man/parent.Rd
man/partial_id_to_name.Rd
man/phylostratr.Rd
man/plot.CountMatrix.Rd
man/plot.Strata.Rd
man/plot_heatmaps.Rd
man/plot_phyloheatmap.Rd
man/plot_proteome_lengths.Rd
man/plot_proteome_stats.Rd
man/print.Strata.Rd
man/proteome_report_table.Rd
man/proteome_stats_table.Rd
man/prune.Rd
man/prune_phylostrata.Rd
man/query_sparql.Rd
man/read_blast.Rd
man/rename_species.Rd
man/replace_branch.Rd
man/result_tree_to_homolog_tree.Rd
man/result_tree_to_pvalue_tree.Rd
man/run_blastp.Rd
man/run_diamond_blastp.Rd
man/run_hmmscan.Rd
man/saccharomyces.Rd
man/set_node_names.Rd
man/sister_trees.Rd
man/sisters.Rd
man/sort_strata.Rd
man/species_to_species_tree.Rd
man/species_tree_to_data_tree.Rd
man/standardize_strata.Rd
man/strata_apply.Rd
man/strata_besthits.Rd
man/strata_blast.Rd
man/strata_convert.Rd
man/strata_diamond.Rd
man/strata_from_blast_dir.Rd
man/strata_from_taxids.Rd
man/strata_map.Rd
man/strata_uniprot_pfam_map.Rd
man/stratify.Rd
man/subset_fasta.Rd
man/subtree.Rd
man/t.CountMatrix.Rd
man/thin_fasta.Rd
man/tree2edgelist.Rd
man/tree_names.Rd
man/tree_size.Rd
man/uniprot_add_idmap.Rd
man/uniprot_downstream_ids.Rd
man/uniprot_fill_strata.Rd
man/uniprot_map2pfam.Rd
man/uniprot_organelle_ids.Rd
man/uniprot_retrieve_proteome.Rd
man/uniprot_retrieve_proteome_table.Rd
man/uniprot_sample_prokaryotes.Rd
man/uniprot_strata.Rd
man/uniprot_weight_by_ref.Rd
man/use_recommended_prokaryotes.Rd
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/sample_data/a.faa
tests/testthat/sample_data/b.faa
tests/testthat/sample_data/blast-header-missing_col.tab
tests/testthat/sample_data/blast-header-no_taxid.tab
tests/testthat/sample_data/blast-header-taxid.tab
tests/testthat/sample_data/blast-no_header-no_taxid.tab
tests/testthat/sample_data/blast-no_header-taxid.tab
tests/testthat/sample_data/c.faa
tests/testthat/sample_data/d.faa
tests/testthat/sample_data/e.faa
tests/testthat/test-blast.R.R
tests/testthat/test-diamond.R.R
tests/testthat/test-diversity-algo.R
tests/testthat/test-read_blast.R
tests/testthat/test-strata.R.R
tests/testthat/test-tree_build.R.R
tests/testthat/test-tree_manipulation.R.R
tests/testthat/test-uniprot.R.R
vignettes/.gitignore
vignettes/arabidopsis.Rmd
vignettes/yeast.Rmd
