Man pages for HuaZou/MicrobiomeAnalysis
Data analysis toolkits in metagenomics
| 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 |
| calculate_geometricmean_abundance | Calculate the Mean abundance of features per group (two... |
| calculate_mean_abundance | Calculate the Mean abundance of features per group (two... |
| calculate_MeanRank_abundance | Calculate the Rank Mean abundance of features per group(two... |
| calculate_median_abundance | Calculate the Median abundance of features per group (two... |
| calculate_occurrence_taxa | Calculate the Occurrence of features per group (two groups) |
| check_sample_names | check whether samples' names start with numeric and then... |
| confounder | Confounder analysis |
| data-caporaso | 16S rRNA data from "Moving pictures of the human microbiome" |
| data-ecam | Data from Early Childhood Antibiotics and the Microbiome... |
| data-enterotypes_arumugam | Enterotypes data of 39 samples |
| data-Zeybel_2022_gut | gut microbiota from Zeybel et al. - 2022 paper |
| data-Zeybel_2022_gut_paired | Paired gut microbiota from Zeybel et al. - 2022 paper |
| data-Zeybel_2022_metabolite | fecal metabolites from Zeybel et al. - 2022 paper |
| data-Zeybel_2022_metabolite_paired | Paired fecal metabolites from Zeybel et al. - 2022 paper |
| data-Zeybel_2022_oral | oral microbiota from Zeybel et al. - 2022 paper |
| data-Zeybel_2022_oral_paired | Paired oral microbiota from Zeybel et al. - 2022 paper |
| data-Zeybel_2022_protein | serum protein from Zeybel et al. - 2022 paper |
| data-Zeybel_2022_protein_paired | Paired serum protein from Zeybel et al. - 2022 paper |
| default_color | generate multiple colors for visualization |
| extract-methods | Extract 'marker_table' object |
| filter_abundance | Filtering feature who is low relative abundance or... |
| get_alphaindex | Calculating index of Alpha diversity on microbiota data |
| get_eigValue | Extract and visualize the eigenvalues/variances of dimensions |
| get_GUniFrac | Generalized UniFrac distances for comparing microbial... |
| import_dada2 | Convert the output of dada2 into phyloseq object |
| import_qiime2 | Convert the qiime2 output of dada2 into phyloseq object |
| import_SE | Convert inputs into SummarizedExperiment object |
| impute_abundance | Imputation methods on missing value |
| insertCol | Insert Row into a Matrix |
| insertRow | Insert Row into a Matrix |
| 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 |
| 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_ord | Visualization of Ordination results with scatterplot |
| plot_volcano | plot the differential analysis results by volcano plot |
| 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_ANOSIM | Analysis of Similarity (ANOSIM) |
| run_betadisper | Multivariate homogeneity of groups dispersions (variances) |
| run_CI | Confidence Interval |
| run_deseq2 | Perform DESeq differential analysis |
| run_distance | Calculate the distance among samples |
| run_edger | Perform differential analysis using edgeR |
| run_group.CI | Group Confidence Interval |
| run_group.STDERR | Group Standard Error Interval |
| run_lefse | Liner discriminant analysis (LDA) effect size (LEFSe)... |
| run_limma_voom | Differential analysis using limma-voom |
| run_MANTEL | Mantel Test (MANTEL) |
| run_marker | Find makers (differentially expressed metagenomic features) |
| run_metabolomeDA | Perform differential analysis on metabolomic data |
| run_metagenomeseq | metagenomeSeq differential analysis |
| run_MRPP | Multi-response Permutation Procedures (MRPP) |
| run_OddRatio | 95% confidential interval Odds Ratio |
| run_ord | Ordination for microbiota data |
| run_PERMANOVA | Permutational multivariate analysis of variance (PERMANOVA) |
| run_simple_stat | Simple statistical analysis of metagenomic profiles |
| run_sl | Identify biomarkers using supervised leaning (SL) methods |
| run_STDERR | Standard Error |
| run_summarySE | Summarizes data for mean median sd etc |
| run_test_multiple_groups | Statistical test for multiple groups |
| run_test_two_groups | Statistical test between two groups |
| scale_variables | Data scaling adjusts each variable/feature |
| subset_marker | Subset microbiome markers |
| summarize_taxa | Summarize taxa into a taxonomic level within each sample |
| transform_abundances | Transform the abundances in 'profile' sample by sample |
| trim_prevalence | Trimming samples or features whose prevalence is less than... |
