Man pages for yiluheihei/microbiomeMarker
microbiome biomarker analysis toolkit
| abundances-methods | Extract taxa abundances |
| aggregate_taxa | Aggregate Taxa |
| assign-marker_table | Assign marker_table to 'object' |
| assign-otu_table | Assign a new OTU table |
| compare_DA | Comparing the results of differential analysis methods by... |
| confounder | Confounder analysis |
| data-caporaso | 16S rRNA data from "Moving pictures of the human microbiome" |
| data-cid_ying | 16S rRNA data of 94 patients from CID 2012 |
| data-ecam | Data from Early Childhood Antibiotics and the Microbiome... |
| data-enterotypes_arumugam | Enterotypes data of 39 samples |
| data-kostic_crc | Data from a study on colorectal cancer (kostic 2012) |
| data-oxygen | Oxygen availability 16S dataset, of which taxa table has been... |
| data-pediatric_ibd | IBD stool samples |
| data-spontaneous_colitis | This is a sample data from lefse python script, a 16S dataset... |
| effect_size-plot | bar and dot plot of effect size of microbiomeMarker data |
| extract-methods | Extract 'marker_table' object |
| extract_posthoc_res | Extract results from a posthoc test |
| get_treedata_phyloseq | Generate tree data from phyloseq object |
| import_dada2 | Import function to read the the output of dada2 as phyloseq... |
| import_picrust2 | Import function to read the output of picrust2 as phyloseq... |
| import_qiime2 | Import function to read the the output of dada2 as phyloseq... |
| marker_table-class | The S4 class for storing microbiome marker information |
| marker_table-methods | Build or access the marker_table |
| microbiomeMarker | Build microbiomeMarker-class objects |
| microbiomeMarker-class | The main class for microbiomeMarker data |
| microbiomeMarker-package | microbiomeMarker: A package for microbiome biomarker... |
| nmarker-methods | Get the number of microbiome markers |
| normalize-methods | Normalize the microbial abundance data |
| phyloseq2DESeq2 | Convert 'phyloseq-class' object to 'DESeqDataSet-class'... |
| phyloseq2edgeR | Convert phyloseq data to edgeR 'DGEList' object |
| phyloseq2metagenomeSeq | Convert phyloseq data to MetagenomeSeq 'MRexperiment' object |
| plot_abundance | plot the abundances of markers |
| plot_cladogram | plot cladogram of micobiomeMaker results |
| plot.compareDA | Plotting DA comparing result |
| plot_heatmap | Heatmap of microbiome marker |
| plot_postHocTest | 'postHocTest' plot |
| plot_sl_roc | ROC curve of microbiome marker from supervised learning... |
| postHocTest | Build postHocTest object |
| postHocTest-class | The postHocTest Class, represents the result of post-hoc test... |
| reexports | Objects exported from other packages |
| run_aldex | Perform differential analysis using ALDEx2 |
| run_ancom | Perform differential analysis using ANCOM |
| run_ancombc | Differential analysis of compositions of microbiomes with... |
| run_deseq2 | Perform DESeq differential analysis |
| run_edger | Perform differential analysis using edgeR |
| run_lefse | Liner discriminant analysis (LDA) effect size (LEFSe)... |
| run_limma_voom | Differential analysis using limma-voom |
| run_marker | Find makers (differentially expressed metagenomic features) |
| run_metagenomeseq | metagenomeSeq differential analysis |
| run_posthoc_test | Post hoc pairwise comparisons for multiple groups test. |
| run_simple_stat | Simple statistical analysis of metagenomic profiles |
| run_sl | Identify biomarkers using supervised leaning (SL) methods |
| run_test_multiple_groups | Statistical test for multiple groups |
| run_test_two_groups | Statistical test between two groups |
| subset_marker | Subset microbiome markers |
| summarize_taxa | Summarize taxa into a taxonomic level within each sample |
| summary.compareDA | Summary differential analysis methods comparison results |
| transform_abundances | Transform the taxa abundances in 'otu_table' sample by sample |
