Files in metacoder
Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/RcppExports.R
R/old_taxa--dataset_documentation.R
R/old_taxa--taxmap--option_parsers.R
R/heat_tree--legend.R
R/old_taxa--globals.R
R/old_taxa--taxon_id.R
R/old_taxa--taxmap--internal.R
R/mothur.R
R/internal.R
R/old_taxa--hierarchies.R
R/heat_tree--resizing_text.R
R/metacoder-package.R
R/old_taxa--taxonomy--internal.R
R/old_taxa--package.R
R/heat_tree--internal.R
R/heat_tree_matrix.R
R/old_taxa--temp.R
R/old_taxa--lazyhelpers.R
R/heat_tree--mapping.R
R/option_parsers.R
R/old_taxa--taxmap--parsers.R
R/old_taxa--taxmap--class.R
R/old_taxa--taxonomy--class.R
R/heat_tree.R
R/parsers.R
R/dataset_documentation.R
R/old_taxa--taxon.R
R/old_taxa--taxmap--s3.R
R/old_taxa--imports.R
R/remove_ambiguous.R
R/read_fasta.R
R/old_taxa--zzz.R
R/old_taxa--taxonomy--docs.R
R/tools.R
R/old_taxa--internal.R
R/heat_tree--vertex_size.R
R/old_taxa--taxon_database.R
R/old_taxa--taxon_name.R
R/calculations--internal.R
R/old_taxa--taxa.R
R/old_taxa--taxmap--docs.R
R/primersearch.R
R/calculations.R
R/old_taxa--taxonomy--s3.R
R/old_taxa--taxmap--printers.R
R/calculations--differential_abundance.R
R/as_phyloseq.R
R/old_taxa--taxon_rank.R
R/old_taxa--hierarchy.R
R/imports.R
R/heat_tree--shape_generators.R
R/startup.R
R/sequence_download.R
R/heat_tree--layouts.R
R/writers.R
src/RcppExports.cpp
src/repel_boxes.cpp
inst/CITATION
inst/doc/introduction.html
inst/doc/introduction.Rmd
inst/extdata/silva_subset.fa
build/vignette.rds
tests/testthat.R
tests/testthat/test--calculations.R
tests/testthat/test-taxon_id.R
tests/testthat/test--taxmap_parsers.R
tests/testthat/test--taxonomy.R
tests/testthat/test--taxa.R
tests/testthat/test--heat_tree.R
tests/testthat/test--parsers_and_writers.R
tests/testthat/test-taxon.R
tests/testthat/test--simulated_pcr.R
tests/testthat/test-taxon_rank.R
tests/testthat/test--taxmap.R
tests/testthat/test-taxon_name.R
tests/testthat/example_data/silva_example.fa
tests/testthat/example_data/dada2.RData
tests/testthat/example_data/nexus_example_1.nex
tests/testthat/example_data/mothur_summary.txt
tests/testthat/example_data/unite_general.fa
tests/testthat/example_data/gg_tax_example.txt
tests/testthat/example_data/newick_example_1.txt
tests/testthat/example_data/rdp_example.fa
tests/testthat/example_data/small_abund_mat.tsv
tests/testthat/example_data/gg_seq_example.fa
vignettes/introduction.Rmd
data/hmp_otus.rda
data/ex_taxmap.rda
data/hmp_samples.rda
data/ranks_ref.rda
man/leaves.Rd
man/my_print.Rd
man/DNAbin_to_char.Rd
man/n_leaves_1.Rd
man/add_alpha.Rd
man/taxa-package.Rd
man/read_fasta.Rd
man/can_be_used_in_taxmap.Rd
man/get_database_name.Rd
man/read_lines_apply.Rd
man/check_taxmap_data.Rd
man/transmute_obs.Rd
man/get_expected_data.Rd
man/parse_raw_heirarchies_to_taxonomy.Rd
man/sample_frac_taxa.Rd
man/quantative_palette.Rd
man/validate_taxmap_funcs.Rd
man/calc_n_samples.Rd
man/validate_regex_match.Rd
man/make_fasta_with_u_replaced.Rd
man/desc_font.Rd
man/ex_taxmap.Rd
man/n_supertaxa_1.Rd
man/scale_bar_coords.Rd
man/starts_with.Rd
man/write_rdp.Rd
man/do_calc_on_num_cols.Rd
man/parse_silva_fasta.Rd
man/ranks_ref.Rd
man/get_taxmap_cols.Rd
man/to_percent.Rd
man/parse_greengenes.Rd
man/count_capture_groups.Rd
man/print__matrix.Rd
man/parse_phyloseq.Rd
man/taxon.Rd
man/sample_frac_obs.Rd
man/rarefy_obs.Rd
man/get_class_from_el.Rd
man/print__logical.Rd
man/primersearch_raw.Rd
man/select_obs.Rd
man/make_dada2_tax_table.Rd
man/ambiguous_patterns.Rd
man/counts_to_presence.Rd
man/calc_obs_props.Rd
man/classifications.Rd
man/print__default_.Rd
man/parse_possibly_named_logical.Rd
man/parse_ubiome.Rd
man/reverse.Rd
man/print_item.Rd
man/init_taxmap_data.Rd
man/edge_list_depth.Rd
man/sample_n_obs.Rd
man/line_coords.Rd
man/is_ambiguous.Rd
man/make_plot_legend.Rd
man/calc_prop_samples.Rd
man/convert_base.Rd
man/is_branch.Rd
man/taxonomy_table.Rd
man/hmp_otus.Rd
man/extract_tax_data.Rd
man/hierarchy.Rd
man/contains.Rd
man/taxon_id.Rd
man/all_functions.Rd
man/write_greengenes.Rd
man/taxon_ranks.Rd
man/verify_label_count.Rd
man/replace_taxon_ids.Rd
man/polygon_coords.Rd
man/supertaxa.Rd
man/parse_unite_general.Rd
man/taxonomy.Rd
man/verify_size_range.Rd
man/progress_lapply.Rd
man/taxon_rank.Rd
man/id_classifications.Rd
man/parse_primersearch.Rd
man/obs.Rd
man/inverse.Rd
man/print__numeric.Rd
man/length_of_thing.Rd
man/make_dada2_asv_table.Rd
man/taxon_names.Rd
man/highlight_taxon_ids.Rd
man/get_data.Rd
man/fasta_headers.Rd
man/get_sort_var.Rd
man/n_supertaxa.Rd
man/validate_regex_key_pair.Rd
man/parse_seq_input.Rd
man/text_grob_length.Rd
man/error_font.Rd
man/rescale.Rd
man/name_font.Rd
man/verify_size.Rd
man/ex_hierarchy2.Rd
man/get_taxmap_other_cols.Rd
man/print_tree.Rd
man/primersearch_is_installed.Rd
man/dot-onAttach.Rd
man/matches.Rd
man/get_node_children.Rd
man/taxa.Rd
man/ex_hierarchies.Rd
man/map_unique.Rd
man/multi_sep_split.Rd
man/capitalize.Rd
man/print__character.Rd
man/split_by_level.Rd
man/taxon_indexes.Rd
man/molten_dist.Rd
man/parse_tax_data.Rd
man/arrange_taxa.Rd
man/calc_taxon_abund.Rd
man/database_list.Rd
man/map_data.Rd
man/subtaxa.Rd
man/print__integer.Rd
man/check_option_groups.Rd
man/internodes.Rd
man/parse_phylo.Rd
man/filter_ambiguous_taxa.Rd
man/select_labels.Rd
man/sample_n_taxa.Rd
man/print__tbl_df.Rd
man/map_data_.Rd
man/n_leaves.Rd
man/n_subtaxa.Rd
man/get_taxmap_table.Rd
man/parse_newick.Rd
man/simplify.Rd
man/look_for_na.Rd
man/label_bounds.Rd
man/rev_comp.Rd
man/get_taxmap_data.Rd
man/layout_functions.Rd
man/apply_color_scale.Rd
man/unique_mapping.Rd
man/limited_print.Rd
man/calc_group_median.Rd
man/parse_heirarchies_to_taxonomy.Rd
man/calc_group_stat.Rd
man/grapes-greater-than-grapes.Rd
man/parse_dataset.Rd
man/as_id.Rd
man/mutate_obs.Rd
man/write_unite_general.Rd
man/n_obs_1.Rd
man/tid_font.Rd
man/taxmap.Rd
man/is_internode.Rd
man/parse_qiime_biom.Rd
man/parse_dada2.Rd
man/parse_edge_list.Rd
man/get_data_frame.Rd
man/obs_apply.Rd
man/stems.Rd
man/verify_taxmap.Rd
man/get_numerics.Rd
man/check_for_pkg.Rd
man/one_of.Rd
man/get_numeric_cols.Rd
man/remove_redundant_names.Rd
man/print__vector.Rd
man/is_root.Rd
man/taxon_name.Rd
man/startup_msg.Rd
man/hmp_samples.Rd
man/parse_summary_seqs.Rd
man/qualitative_palette.Rd
man/data_used.Rd
man/run_primersearch.Rd
man/ex_hierarchy3.Rd
man/print__factor.Rd
man/roots.Rd
man/zero_low_counts.Rd
man/filter_obs.Rd
man/is_stem.Rd
man/lookup_tax_data.Rd
man/hierarchies.Rd
man/n_obs.Rd
man/compare_groups.Rd
man/taxon_database.Rd
man/names_used.Rd
man/verify_trans.Rd
man/ambiguous_synonyms.Rd
man/get_optimal_range.Rd
man/parse_rdp.Rd
man/prefixed_print.Rd
man/num_range.Rd
man/write_silva_fasta.Rd
man/subtaxa_apply.Rd
man/all_names.Rd
man/primersearch.Rd
man/calc_group_mean.Rd
man/supertaxa_apply.Rd
man/ends_with.Rd
man/ncbi_sequence.Rd
man/leaves_apply.Rd
man/diverging_palette.Rd
man/ex_hierarchy1.Rd
man/get_taxonomy_levels.Rd
man/heat_tree_matrix.Rd
man/complement.Rd
man/ncbi_taxon_sample.Rd
man/can_be_num.Rd
man/punc_font.Rd
man/transform_data.Rd
man/taxon_ids.Rd
man/n_subtaxa_1.Rd
man/check_element_length.Rd
man/verify_color_range.Rd
man/metacoder.Rd
man/heat_tree.Rd
man/correct_taxon_names.Rd
man/calc_group_rsd.Rd
man/get_dataset.Rd
man/repo_url.Rd
man/get_edge_children.Rd
man/is_leaf.Rd
man/get_edge_parents.Rd
man/arrange_obs.Rd
man/print__ordered.Rd
man/filter_taxa.Rd
man/print__list.Rd
man/parse_mothur_taxonomy.Rd
man/as_phyloseq.Rd
man/print__data.frame.Rd
man/check_class_col.Rd
man/filtering-helpers.Rd
man/calc_diff_abund_deseq2.Rd
man/inter_circle_gap.Rd
man/get_dots_or_list.Rd
man/branches.Rd
man/write_mothur_taxonomy.Rd
man/parse_mothur_tax_summary.Rd
man/everything.Rd
man/figures/readme_figure.jpg
