# Lightweight One-Line Resolving Microbial Ecology Program

## Documentation for package ‘LorMe’ version 2.0.1

- DESCRIPTION file.

## Help Pages

LorMe-package | LorMe: Lightweight One-Line Resolving Microbial Ecology Program
$-method | Access LorMe object elements via $
.DollarNames.LorMe | Tab completion for LorMe $ access
.LorMe_opts | Global options for LorMe pipeline analysis
.onLoad | Accessed by 'getOption("LorMe")' or 'LorMe_options()'
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 dataframe table
anova_report | Print Analysis of Variance report
auto_signif_test | Automatic significance test
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 Object
compare_plot | Comparison plot generator This function help generate comparsion plot including bar plot, box plot, and violin plot
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
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 | LorMe: Lightweight One-Line Resolving Microbial Ecology Program
LorMe-class | LorMe S4 class
LorMe_defaults | Restore LorMe global options to factory defaults
LorMe_options | Change LorMe options
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_withdiff | Network Analysis with Differential Species
object_config | Set taxonomy summary configuration
safe_run | Running function with safe mode
show-method | Show method for LorMe objects
structure_plot | Visualize microbial community composition structure based on tax summary object
sub_tax_summary | Subsetting tax summary objects
tax_summary | Encapsulate meta file, feature tables and taxonomy annotation into tax summary object
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
Two_group | Tax summary object with two groups
t_test_report | Print Student's t-Test report
volcano_plot | Generate Volcano plot base on Deseq_analysis or indicator_analysis results
wilcox_test_report | Print Wilcoxon Rank Sum and Signed Rank Tests reprot