Man pages for LorMe
Lightweight One-Line Resolving Microbial Ecology Program
| add_tree | Attach phylogenetic tree to the LorMe object |
| Alpha_diversity_calculator | Calculate alpha diversity based on tax summary object |
| Alpha_diversity_calculator2 | Calculate alpha diversity based on tax summary object or... |
| anova_report | Print Analysis of Variance report |
| auto_signif_test | Automatic significance test |
| cash-LorMe-method | Access LorMe object elements via $ |
| circulation_lm | Circulation of fitting Linear Models |
| color_scheme | Get color scheme |
| combine_and_translate | Combine data for visualization |
| community_plot | Generate Community Composition Plot Based on Tax_summary... |
| compare_plot | Comparison plot generator This function help generate... |
| Deseq_analysis | Deseq Analysis Function |
| Deseq_analysis2 | Deseq analysis |
| differential_bar | Generate Differential Bar Plot and Error bar Plot |
| Dimension_reduction | Dimension_reduction: PCA, PCOA, and NMDS Analysis |
| dot-DollarNames.LorMe | Tab completion for LorMe $ access |
| dot-LorMe_opts | Global options for LorMe pipeline analysis |
| dot-onLoad | Accessed by 'getOption("LorMe")' or 'LorMe_options()' |
| Facet_group | Tax summary object with Facet 2x2 Groups |
| Filter_function | Filter OTU/ASV/metagenomic profile/gene profile by threshold |
| indicator_analysis | Indicator Analysis |
| kruskal_report | Print Kruskal-Wallis Rank Sum Test report |
| LorMe-class | LorMe S4 class |
| LorMe_defaults | Restore LorMe global options to factory defaults |
| LorMe_options | Change LorMe options |
| LorMe-package | LorMe: Lightweight One-Line Resolving Microbial Ecology... |
| LorMe_pipeline | One-stop microbial analysis pipeline for LorMe objects |
| manhattan | Manhattan Plot Generator |
| Module_abundance | Calculate network module abundance for each sample |
| Module_composition | Pie chart for network module composition |
| nc | Calculate Network Natural Connectivity |
| NC_remove | Natural connectivity analysis |
| network_analysis | Conduct Network analysis based on tax summary object |
| network_analysis2 | Conduct Network analysis |
| network_stat | Igraph network statistics |
| network_visual | Network Visualization |
| network_visual_re | Re-visualize network plot from 'network_visual' or... |
| network_withdiff | Network Analysis with Differential Species |
| object_config | Set taxonomy summary configuration |
| safe_run | Running function with safe mode |
| show-LorMe-method | Show method for LorMe objects |
| structure_plot | Visualize microbial community composition structure based on... |
| sub_tax_summary | Subsetting tax summary objects |
| tax_summary | Encapsulate meta file, feature tables and taxonomy annotation... |
| tbRDA_analysis | tbRDA analysis |
| testotu | test otudata |
| theme_zg | A classic theme for ggplot |
| Three_group | Tax summary object with three groups |
| Top_taxa | Calculate top taxa and others |
| Trans_from_microeco | Convert a microeco object to a LorMe object |
| Trans_from_phylo | Convert phyloseq object to LorMe object |
| Trans_to_microeco | Convert a LorMe object to a microeco object |
| Trans_to_phylo | Convert a LorMe object to a phyloseq object |
| t_test_report | Print Student's t-Test report |
| Two_group | Tax summary object with two groups |
| volcano_plot | Generate Volcano plot base on Deseq_analysis or... |
| wilcox_test_report | Print Wilcoxon Rank Sum and Signed Rank Tests reprot |
