R: Work with QIIME Output Files in R

# Work with QIIME Output Files in R

## Documentation for package ‘qiimer’ version 0.9.4

- DESCRIPTION file.

## Help Pages

qiimer-package | qiimer: Read QIIME output files and create plots
biom_raw_data | Extract raw data from a BIOM object.
biom_taxonomy | Extract taxonomy info from a biom object.
dist_get | Retrieve distances from a '"dist"' object.
dist_groups | Create a data frame of distances between groups of items.
dist_subset | Extract parts of a '"dist"' object.
make_otu_table | Create an OTU table.
otu_heatmap | Create a heatmap of OTU counts.
qiimer | qiimer: Read QIIME output files and create plots
rarefaction_stats | Compute summary statistics for collated alpha diversity tables.
read_blast_table | Parse tabular output from BLAST.
read_qiime_distmat | Read a QIIME distance matrix file.
read_qiime_mapping_file | Read a QIIME sample mapping file.
read_qiime_otu_mapping | Parse an OTU mapping file from QIIME.
read_qiime_otu_table | Parse a QIIME OTU table file in "calssic" format.
read_qiime_rarefaction | Read a collated alpha diversity table from QIIME.
relmbeta | Sample dataset from murine gut microbiome
relmbeta_alpha | Shannon diversity measurements from murine gut microbiome
relmbeta_assignments | Taxonomic assignments from murine gut microbiome
relmbeta_biom | BIOM format object from murine gut microbiome
relmbeta_counts | OTU counts from murine gut microbiome
relmbeta_dist | Unweighted UniFrac distances from murine gut microbiome
saturated_rainbow | Saturated rainbow palette.
simplify_assignments | Reformat taxonomic assignments for presentation.
split_assignments | Split taxonomic assignment strings
taxonomic_ranks | Standard taxonomic ranks.