Man pages for kylebittinger/qiimer
Work with QIIME Output Files in R
| 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... |
| 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. |
