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metacoder  

Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
View on CRAN: Click here


Download and install metacoder package within the R console
Install from CRAN:
install.packages("metacoder")

Install from Github:
library("remotes")
install_github("cran/metacoder")

Install by package version:
library("remotes")
install_version("metacoder", "0.3.8")



Attach the package and use:
library("metacoder")
Maintained by
Zachary Foster
[Scholar Profile | Author Map]
First Published: 2016-08-27
Latest Update: 2024-02-20
Description:
A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).
How to cite:
Zachary Foster (2016). metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data. R package version 0.3.8, https://cran.r-project.org/web/packages/metacoder. Accessed 14 Mar. 2025.
Previous versions and publish date:
0.1.2 (2016-08-27 00:35), 0.1.3 (2017-05-23 07:36), 0.2.0 (2018-01-06 00:53), 0.2.1 (2018-05-02 07:45), 0.3.0.1 (2018-11-19 09:36), 0.3.0 (2018-08-28 08:02), 0.3.1 (2019-01-05 00:50), 0.3.2 (2019-04-08 20:40), 0.3.3 (2019-07-18 08:35), 0.3.4 (2020-04-29 21:40), 0.3.5 (2021-06-24 00:00), 0.3.6 (2023-04-04 04:20), 0.3.7 (2024-02-20 10:30)
Other packages that cited metacoder R package
View metacoder citation profile
Other R packages that metacoder depends, imports, suggests or enhances
Complete documentation for metacoder
Functions, R codes and Examples using the metacoder R package
Some associated functions: DNAbin_to_char . add_alpha . all_functions . all_names . ambiguous_patterns . ambiguous_synonyms . apply_color_scale . arrange_obs . arrange_taxa . as_id . as_phyloseq . branches . calc_diff_abund_deseq2 . calc_group_mean . calc_group_median . calc_group_rsd . calc_group_stat . calc_n_samples . calc_obs_props . calc_prop_samples . calc_taxon_abund . can_be_num . can_be_used_in_taxmap . capitalize . check_class_col . check_element_length . check_for_pkg . check_option_groups . check_taxmap_data . classifications . compare_groups . complement . contains . convert_base . correct_taxon_names . count_capture_groups . counts_to_presence . data_used . database_list . desc_font . diverging_palette . do_calc_on_num_cols . dot-onAttach . edge_list_depth . ends_with . error_font . everything . ex_hierarchies . ex_hierarchy1 . ex_hierarchy2 . ex_hierarchy3 . ex_taxmap . extract_tax_data . fasta_headers . filter_ambiguous_taxa . filter_obs . filter_taxa . filtering-helpers . get_class_from_el . get_data . get_data_frame . get_database_name . get_dataset . get_dots_or_list . get_edge_children . get_edge_parents . get_expected_data . get_node_children . get_numeric_cols . get_numerics . get_optimal_range . get_sort_var . get_taxmap_cols . get_taxmap_data . get_taxmap_other_cols . get_taxmap_table . get_taxonomy_levels . grapes-greater-than-grapes . heat_tree . heat_tree_matrix . hierarchies . hierarchy . highlight_taxon_ids . hmp_otus . hmp_samples . id_classifications . init_taxmap_data . inter_circle_gap . internodes . inverse . is_ambiguous . is_branch . is_internode . is_leaf . is_root . is_stem . label_bounds . layout_functions . leaves . leaves_apply . length_of_thing . limited_print . line_coords . look_for_na . lookup_tax_data . make_dada2_asv_table . make_dada2_tax_table . make_fasta_with_u_replaced . make_plot_legend . map_data . map_data_ . map_unique . matches . metacoder . molten_dist . multi_sep_split . mutate_obs . my_print . n_leaves . n_leaves_1 . n_obs . n_obs_1 . n_subtaxa . n_subtaxa_1 . n_supertaxa . n_supertaxa_1 . name_font . names_used . ncbi_sequence . ncbi_taxon_sample . num_range . obs . obs_apply . one_of . parse_dada2 . parse_dataset . parse_edge_list . parse_greengenes . parse_heirarchies_to_taxonomy . parse_mothur_tax_summary . parse_mothur_taxonomy . parse_newick . parse_phylo . parse_phyloseq . parse_possibly_named_logical . parse_primersearch . parse_qiime_biom . parse_raw_heirarchies_to_taxonomy . parse_rdp . parse_seq_input . parse_silva_fasta . parse_summary_seqs . parse_tax_data . parse_ubiome . parse_unite_general . polygon_coords . prefixed_print . primersearch . primersearch_is_installed . primersearch_raw . print__character . print__data.frame . print__default_ . print__factor . print__integer . print__list . print__logical . print__matrix . print__numeric . print__ordered . print__tbl_df . print__vector . print_item . print_tree . progress_lapply . punc_font . qualitative_palette . quantative_palette . ranks_ref . rarefy_obs . read_fasta . read_lines_apply . remove_redundant_names . replace_taxon_ids . repo_url . rescale . rev_comp . reverse . roots . run_primersearch . sample_frac_obs . sample_frac_taxa . sample_n_obs . sample_n_taxa . scale_bar_coords . select_labels . select_obs . simplify . split_by_level . starts_with . startup_msg . stems . subtaxa . subtaxa_apply . supertaxa . supertaxa_apply . taxa-package . taxa . taxmap . taxon . taxon_database . taxon_id . taxon_ids . taxon_indexes . taxon_name . taxon_names . taxon_rank . taxon_ranks . taxonomy . taxonomy_table . text_grob_length . tid_font . to_percent . transform_data . transmute_obs . unique_mapping . validate_regex_key_pair . validate_regex_match . validate_taxmap_funcs . verify_color_range . verify_label_count . verify_size . verify_size_range . verify_taxmap . verify_trans . write_greengenes . write_mothur_taxonomy . write_rdp . write_silva_fasta . write_unite_general . zero_low_counts . 
Some associated R codes: RcppExports.R . as_phyloseq.R . calculations--differential_abundance.R . calculations--internal.R . calculations.R . dataset_documentation.R . heat_tree--internal.R . heat_tree--layouts.R . heat_tree--legend.R . heat_tree--mapping.R . heat_tree--resizing_text.R . heat_tree--shape_generators.R . heat_tree--vertex_size.R . heat_tree.R . heat_tree_matrix.R . imports.R . internal.R . metacoder-package.R . mothur.R . old_taxa--dataset_documentation.R . old_taxa--globals.R . old_taxa--hierarchies.R . old_taxa--hierarchy.R . old_taxa--imports.R . old_taxa--internal.R . old_taxa--lazyhelpers.R . old_taxa--package.R . old_taxa--taxa.R . old_taxa--taxmap--class.R . old_taxa--taxmap--docs.R . old_taxa--taxmap--internal.R . old_taxa--taxmap--option_parsers.R . old_taxa--taxmap--parsers.R . old_taxa--taxmap--printers.R . old_taxa--taxmap--s3.R . old_taxa--taxon.R . old_taxa--taxon_database.R . old_taxa--taxon_id.R . old_taxa--taxon_name.R . old_taxa--taxon_rank.R . old_taxa--taxonomy--class.R . old_taxa--taxonomy--docs.R . old_taxa--taxonomy--internal.R . old_taxa--taxonomy--s3.R . old_taxa--temp.R . old_taxa--zzz.R . option_parsers.R . parsers.R . primersearch.R . read_fasta.R . remove_ambiguous.R . sequence_download.R . startup.R . tools.R . writers.R .  Full metacoder package functions and examples
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