API for yiluheihei/microbiomeMarker
microbiome biomarker analysis toolkit
| Global functions | |
|---|---|
| %>% | Man page |
| .plot_ef | Source code |
| .sum_consensus | Source code |
| .summarize_taxa_level | Source code |
| Contrasts | Source code |
| [ | Man page |
| [,marker_table,ANY,ANY,ANY-method | Man page |
| abundances | Man page |
| abundances, | Man page |
| abundances,microbiomeMarker-method | Man page |
| abundances,otu_table-method | Man page |
| abundances,phyloseq-method | Man page |
| add_missing_levels | Source code |
| add_prefix | Source code |
| add_prefix_summarized | Source code |
| aggregate_taxa | Man page Source code |
| aldex_kw | Source code |
| aldex_t | Source code |
| assign-marker_table | Man page |
| assign-otu_table | Man page |
| bootstap_lda | Source code |
| bootstap_lda_one | Source code |
| bootstrap_diff_mean_prop_single | Source code |
| cal_pair_lda | Source code |
| calc_ancom_p | Source code |
| calc_ancom_pmat | Source code |
| calc_bootstrap_ci | Source code |
| calc_coef | Source code |
| calc_ef_md_f | Source code |
| calc_games_howell_test | Source code |
| calc_p_large_sample | Source code |
| calc_permute_p | Source code |
| calc_permute_ts | Source code |
| calc_ratio | Source code |
| calc_scheffe_test | Source code |
| calc_sparse_diff_mean | Source code |
| calc_sparse_p | Source code |
| calc_tukey_test | Source code |
| calc_twosample_ts | Source code |
| calc_twosample_ts_single_feature | Source code |
| calc_welch_uncorrected_test | Source code |
| caporaso | Man page |
| check_bootstrap_sample | Source code |
| check_confounder | Source code |
| check_contrast | Source code |
| check_rank_names | Source code |
| check_samples | Source code |
| check_tax_prefix | Source code |
| check_tax_summarize | Source code |
| check_taxa_rank | Source code |
| check_var_in_meta | Source code |
| cid_ying | Man page |
| compare_DA | Man page Source code |
| confounder | Man page Source code |
| convert_instance | Source code |
| create_contingency_matrix | Source code |
| create_design | Source code |
| create_ps_from_mm | Source code |
| data-caporaso | Man page |
| data-cid_ying | Man page |
| data-ecam | Man page |
| data-enterotypes_arumugam | Man page |
| data-kostic_crc | Man page |
| data-oxygen | Man page |
| data-pediatric_ibd | Man page |
| data-spontaneous_colitis | Man page |
| ecam | Man page |
| ef-barplot,ef-dotplot | Man page |
| enterotypes_arumugam | Man page |
| estimateSizeFactorsForMatrix | Source code |
| extract_posthoc_res | Man page Source code |
| extract_prefix | Source code |
| extract_rank | Source code |
| fix_duplicate_tax | Source code |
| fix_na_tax | Source code |
| generate_cladogram_annotation | Source code |
| generate_compare_args | Source code |
| generate_taxa_tree | Source code |
| get_aldex_kwglm_enrich_group | Source code |
| get_ancom_enrich_group | Source code |
| get_ancombc_enrich_group | Source code |
| get_angle | Source code |
| get_available_prefix | Source code |
| get_feature_enrich_group | Source code |
| get_feature_label | Source code |
| get_features_labels | Source code |
| get_mgs_enrich_group | Source code |
| get_norm_factors | Source code |
| get_norm_method | Source code |
| get_offset | Source code |
| get_prefix | Source code |
| get_short_label_id | Source code |
| get_sig_annotation | Source code |
| get_sig_annotation_single | Source code |
| get_sl_enrich_group | Source code |
| get_struc_zero | Source code |
| get_treedata_phyloseq | Man page Source code |
| get_unique_id | Source code |
| gm_mean | Source code |
| has_prefix | Source code |
| import_biobakery_lefse_in | Source code |
| import_biom | Man page |
| import_dada2 | Man page Source code |
| import_mothur | Man page |
| import_picrust2 | Man page Source code |
| import_qiime | Man page |
| import_qiime2 | Man page Source code |
| is_dna_seq | Source code |
| is_picrust2 | Source code |
| keep_prefix_desc | Source code |
| keep_taxa_in_rows | Source code |
| kostic_crc | Man page |
| lefse_format_grp | Source code |
| marker_table | Man page |
| marker_table,data.frame-method | Man page |
| marker_table,microbiomeMarker-method | Man page |
| marker_table-class | Man page |
| marker_table<- | Man page |
| microbiomeMarker | Man page Source code |
| microbiomeMarker-class | Man page |
| microbiomeMarker-package | Man page |
| nmarker | Man page |
| nmarker,marker_table-method | Man page |
| nmarker,microbiomeMarker-method | Man page |
| norm_clr | Man page Source code |
| norm_cpm | Man page Source code |
| norm_css | Man page Source code |
| norm_rarefy | Man page Source code |
| norm_rle | Man page Source code |
| norm_tmm | Man page Source code |
| norm_tss | Man page Source code |
| normalize | Man page |
| normalize,data.frame-method | Man page |
| normalize,matrix-method | Man page |
| normalize,otu_table-method | Man page |
| normalize,phyloseq-method | Man page |
| normalize_feature | Source code |
| nsamples | Man page |
| ntaxa | Man page |
| otu_table | Man page |
| otu_table-method | Man page |
| otu_table2metagenomeSeq | Man page Source code |
| otu_table<-,microbiomeMarker,microbiomeMarker-method | Man page |
| otu_table<-,microbiomeMarker,otu_table-method | Man page |
| otu_table<-,microbiomeMarker,phyloseq-method | Man page |
| oxygen | Man page |
| parse_q2taxonomy | Source code |
| pediatric_ibd | Man page |
| phyloseq2DESeq2 | Man page Source code |
| phyloseq2edgeR | Man page Source code |
| phyloseq2metagenomeSeq | Man page Source code |
| phyloseq_qc | Source code |
| plot.compareDA | Man page Source code |
| plot_abundance | Man page Source code |
| plot_cladogram | Man page Source code |
| plot_ef_bar | Man page Source code |
| plot_ef_dot | Man page Source code |
| plot_heatmap | Man page Source code |
| plot_postHocTest | Man page Source code |
| plot_sl_roc | Man page Source code |
| postHocTest | Man page Source code |
| postHocTest-class | Man page |
| postHocTest-method | Man page |
| pre_ps_taxa_rank | Source code |
| preprocess_ancom | Source code |
| preprocess_feature | Source code |
| preprocess_feature_all | Source code |
| preprocess_ps | Source code |
| pvalue2siglevel | Source code |
| read_q2biom | Source code |
| read_q2sample_meta | Source code |
| read_q2taxa | Source code |
| read_qza | Source code |
| reexports | Man page |
| remove_na_samples | Source code |
| replace_unknown_species | Source code |
| return_marker | Source code |
| run_aldex | Man page Source code |
| run_ancom | Man page Source code |
| run_ancombc | Man page Source code |
| run_deseq2 | Man page Source code |
| run_edger | Man page Source code |
| run_lefse | Man page Source code |
| run_limma_voom | Man page Source code |
| run_marker | Man page Source code |
| run_metagenomeseq | Man page Source code |
| run_posthoc_test | Man page Source code |
| run_simple_stat | Man page Source code |
| run_sl | Man page Source code |
| run_t_test | Source code |
| run_test_multiple_groups | Man page Source code |
| run_test_two_groups | Man page Source code |
| run_white_test | Source code |
| sample_data | Man page |
| sample_names | Man page |
| scale_rows | Source code |
| select_quantile_func | Source code |
| set_lvl | Source code |
| set_marker_annotation | Source code |
| set_nf | Source code |
| show, | Man page |
| show,microbiomeMarker-method | Man page |
| show,postHocTest-method | Man page |
| space | Source code |
| spikein | Source code |
| spontaneous_colitis | Man page |
| standardise_call | Source code |
| subset_marker | Man page Source code |
| subset_taxa_in_feature | Source code |
| summarize_taxa | Man page Source code |
| summary.compareDA | Man page Source code |
| t_fast | Source code |
| tax_table | Man page |
| taxa_names | Man page |
| test_rep_wilcoxon | Source code |
| trans_clr | Source code |
| transform_abundances | Man page Source code |
| transform_log10 | Source code |
| transform_log10p | Source code |
| transpose_and_2df | Source code |
| upper_firstletter | Source code |
| validity_marker_table | Source code |
| validity_microbiomeMarker | Source code |
| validity_postHocTest | Source code |
| wilcox_fast | Source code |
