Files in grunwaldlab/metacoder
Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/RcppExports.R R/calculations--internal.R R/calculations.R R/dataset_documentation.R R/heat_tree--internal.R R/heat_tree--layouts.R R/heat_tree--legend.R R/heat_tree--mapping.R R/heat_tree--resizing_text.R R/heat_tree--shape_generators.R R/heat_tree--vertex_size.R R/heat_tree.R R/heat_tree_matrix.R R/imports.R R/internal.R R/metacoder-package.R R/mothur.R R/option_parsers.R R/parsers.R R/primersearch.R R/read_fasta.R R/remove_ambiguous.R R/sequence_download.R R/startup.R R/tools.R R/writers.R README.Rmd README.md cran-comments.md
data/hmp_otus.rda
data/hmp_samples.rda
hex_sticker/hex_sticker.png
hex_sticker/hex_sticker.svg
hex_sticker/hex_sticker_tree.R
hex_sticker/hex_sticker_tree.svg
inst/CITATION
inst/extdata/.gitignore
inst/extdata/silva_subset.fa
man/DNAbin_to_char.Rd man/add_alpha.Rd man/ambiguous_patterns.Rd man/apply_color_scale.Rd man/calc_group_mean.Rd man/calc_group_median.Rd man/calc_group_rsd.Rd man/calc_group_stat.Rd man/calc_n_samples.Rd man/calc_obs_props.Rd man/calc_prop_samples.Rd man/calc_taxon_abund.Rd man/can_be_num.Rd man/check_element_length.Rd man/check_for_pkg.Rd man/check_option_groups.Rd man/compare_groups.Rd man/complement.Rd man/contains.Rd man/convert_base.Rd man/diverging_palette.Rd man/do_calc_on_num_cols.Rd man/edge_list_depth.Rd man/ends_with.Rd man/everything.Rd man/fasta_headers.Rd
man/figures/README-unnamed-chunk-12-1.png
man/figures/README-unnamed-chunk-15-1.png
man/figures/README-unnamed-chunk-17-1.png
man/figures/README-unnamed-chunk-19-1.png
man/figures/readme_figure.png
man/filter_ambiguous_taxa.Rd man/get_class_from_el.Rd man/get_edge_children.Rd man/get_edge_parents.Rd man/get_node_children.Rd man/get_numeric_cols.Rd man/get_numerics.Rd man/get_optimal_range.Rd man/get_taxmap_cols.Rd man/get_taxmap_data.Rd man/get_taxmap_other_cols.Rd man/get_taxmap_table.Rd man/get_taxonomy_levels.Rd man/grapes-greater-than-grapes.Rd man/heat_tree.Rd man/heat_tree_matrix.Rd man/hmp_otus.Rd man/hmp_samples.Rd man/inter_circle_gap.Rd man/inverse.Rd man/is_ambiguous.Rd man/label_bounds.Rd man/layout_functions.Rd man/limited_print.Rd man/line_coords.Rd man/look_for_na.Rd man/make_plot_legend.Rd man/map_unique.Rd man/matches.Rd man/metacoder.Rd man/molten_dist.Rd man/my_print.Rd man/ncbi_sequence.Rd man/ncbi_taxon_sample.Rd man/num_range.Rd man/one_of.Rd man/parse_greengenes.Rd man/parse_mothur_tax_summary.Rd man/parse_mothur_taxonomy.Rd man/parse_newick.Rd man/parse_phylo.Rd man/parse_phyloseq.Rd man/parse_primersearch.Rd man/parse_qiime_biom.Rd man/parse_rdp.Rd man/parse_seq_input.Rd man/parse_silva_fasta.Rd man/parse_summary_seqs.Rd man/parse_unite_general.Rd man/polygon_coords.Rd man/primersearch.Rd man/primersearch_is_installed.Rd man/qualitative_palette.Rd man/quantative_palette.Rd man/rarefy_obs.Rd man/read_fasta.Rd man/read_lines_apply.Rd man/repo_url.Rd man/rescale.Rd man/rev_comp.Rd man/reverse.Rd man/run_primersearch.Rd man/scale_bar_coords.Rd man/select_labels.Rd man/split_by_level.Rd man/starts_with.Rd man/startup_msg.Rd man/text_grob_length.Rd man/transform_data.Rd man/unique_mapping.Rd man/verify_color_range.Rd man/verify_label_count.Rd man/verify_size.Rd man/verify_size_range.Rd man/verify_taxmap.Rd man/verify_trans.Rd man/write_greengenes.Rd man/write_mothur_taxonomy.Rd man/write_rdp.Rd man/write_silva_fasta.Rd man/write_unite_general.Rd man/zero_low_counts.Rd
metacoder.Rproj
scratch/.gitignore
scratch/arrange_taxa_gc_weirdness.Rmd scratch/default_plotting.Rmd
scratch/example.phyloseq
scratch/figure.svg
scratch/figure_text.Rmd scratch/hmp_example_data.Rmd scratch/in_silico_pcr_data.Rmd scratch/issue_123--warning_for_invalid_class_regex.Rmd scratch/issue_127--heat_tree_inf_usage.Rmd scratch/issue_140.Rmd scratch/issue_141--phyloseq_converter.Rmd scratch/resizing_text_test.Rmd
scratch/silva_subset.fa
scratch/test.RData
scratch/vocabulary.Rmd
src/RcppExports.cpp
src/repel_boxes.cpp
tests/testthat.R
tests/testthat/example_data/gg_seq_example.fa
tests/testthat/example_data/gg_tax_example.txt
tests/testthat/example_data/mothur_summary.txt
tests/testthat/example_data/newick_example_1.txt
tests/testthat/example_data/nexus_example_1.nex
tests/testthat/example_data/rdp_example.fa
tests/testthat/example_data/silva_example.fa
tests/testthat/example_data/small_abund_mat.tsv
tests/testthat/example_data/unite_general.fa
tests/testthat/test--calculations.R tests/testthat/test--heat_tree.R tests/testthat/test--parsers_and_writers.R tests/testthat/test--simulated_pcr.R vignettes/introduction.Rmd
grunwaldlab/metacoder documentation built on May 31, 2018, 7:05 a.m.