API for Gibbons-Lab/mbtools
Provides helper functions for microbiome preprocessing and analysis
| Global functions | |
|---|---|
| .onAttach | Source code |
| ERR260132 | Man page |
| `%p%` | Source code |
| align | Source code |
| align_long_reads | Man page Source code |
| align_short_reads | Man page Source code |
| annotate_contigs | Man page |
| annotate_files | Source code |
| annotate_silva | Man page |
| as.matrix.mbquant | Man page Source code |
| as_phyloseq | Man page Source code |
| association | Man page Source code |
| basecalls | Source code |
| bin_coverage | Man page Source code |
| bracken_to_phyloseq | Man page Source code |
| build_lineage | Man page Source code |
| check_variables | Source code |
| classified_taxa | Source code |
| clean_taxa_names | Source code |
| combinatorial_association | Man page Source code |
| config_align | Man page |
| config_association | Man page |
| config_builder | Source code |
| config_chimera | Man page |
| config_count | Man page |
| config_coverage | Man page |
| config_demultiplex | Man page |
| config_denoise | Man page |
| config_layout | Man page |
| config_parser | Source code |
| config_power | Man page |
| config_preprocess | Man page |
| config_reference | Man page |
| config_rep | Man page |
| config_slimm | Man page |
| config_sra | Man page |
| count_alns | Source code |
| count_med | Source code |
| count_references | Man page |
| demultiplex | Man page Source code |
| denoise | Man page Source code |
| discretize | Man page Source code |
| download_bacterial_transcripts | Man page |
| download_files | Man page Source code |
| download_reads | Source code |
| download_sra | Man page Source code |
| effective_lengths | Man page Source code |
| em_count | Man page Source code |
| entropy | Source code |
| filter_chimeras | Source code |
| filter_counts | Man page Source code |
| filter_reference | Man page Source code |
| find_read_files | Man page Source code |
| find_taxa | Man page Source code |
| getN | Source code |
| get_alignments | Source code |
| get_corncob_pars | Source code |
| get_files | Source code |
| grid | Source code |
| hitdb_cleaner | Source code |
| irep | Source code |
| iter_clr | Source code |
| iter_deseq2 | Source code |
| iter_limma | Source code |
| iter_lm | Source code |
| iter_voom | Source code |
| layout | Man page Source code |
| library_size | Source code |
| mbtools | Man page |
| memory_use | Source code |
| merge_transcripts | Man page |
| mock_plot | Man page Source code |
| mockrobiota | Man page Source code |
| mothur_to_dada | Man page Source code |
| normalize | Man page Source code |
| orlitsky | Man page Source code |
| parse_ensembl_id | Man page |
| parse_threads | Source code |
| plot_bb_fits | Man page Source code |
| plot_counts | Man page Source code |
| plot_entropy | Man page |
| plot_lengths | Man page |
| plot_qualities | Man page |
| plot_taxa | Man page Source code |
| power_analysis | Man page |
| prepare_filelist | Source code |
| preprocess | Man page Source code |
| qualities | Source code |
| quality_control | Man page Source code |
| quality_profile | Man page Source code |
| read_bam | Man page Source code |
| read_blast | Man page Source code |
| read_length | Man page Source code |
| read_slimm | Man page Source code |
| read_slimm_coverage | Man page Source code |
| reads_to_phyloseq | Man page Source code |
| remove_chimeras | Man page Source code |
| remove_reference | Man page Source code |
| replication_rates | Man page Source code |
| select | Man page Source code |
| silent_lib | Source code |
| silva_build_taxonomy | Man page |
| slimm | Man page Source code |
| slimm_files | Man page |
| species_names | Source code |
| split_ext | Source code |
| sra_download_url | Source code |
| sra_filelist | Source code |
| sra_submission | Man page Source code |
| standardize | Man page Source code |
| taxa_count | Man page Source code |
| taxa_metrics | Man page Source code |
| taxa_quants | Man page Source code |
| taxa_str | Source code |
| tool_version | Source code |
| types | Man page Source code |
| unshrink | Source code |
| validate | Source code |
| with_classification | Man page Source code |
