# Lightening One-Code Resolving Microbial Ecology Solution

## Documentation for package ‘LorMe’ version 1.2.0

- DESCRIPTION file.

## Help Pages

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 package: Lightening One-Code Resolving Microbial Ecology Program
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
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
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