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LorMe (version 1.2.1)

Lightening One-Code Resolving Microbial Ecology Solution

Description

Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.

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Version

Install

install.packages('LorMe')

Monthly Downloads

15,494

Version

1.2.1

License

GPL-3

Maintainer

Ningqi Wang

Last Published

March 14th, 2025

Functions in LorMe (1.2.1)

color_scheme

Get color scheme
auto_signif_test

Automatic significance test
Top_taxa

Calculate top taxa and others
circulation_lm

Circulation of fitting Linear Models
Two_group

Tax summary object with two groups
community_plot

Generate Community Composition Plot Based on Tax_summary Object
anova_report

Print Analysis of Variance report
combine_and_translate

Combine data for visualization
NC_remove

Natural connectivity analysis
Three_group

Tax summary object with three groups
network_visual

Network Visualization
nc

Calculate Network Natural Connectivity
network_stat

Igraph network statistics
manhattan

Manhattan Plot Generator
indicator_analysis

Indicator Analysis
network_analysis

Conduct Network analysis based on tax summary object
compare_plot

Comparison plot generator This function help generate comparsion plot including bar plot, box plot, and violin plot
network_analysis2

Conduct Network analysis
kruskal_report

Print Kruskal-Wallis Rank Sum Test report
object_config

Set taxonomy summary configuration
differential_bar

Generate Differential Bar Plot and Error bar Plot
testotu

test otudata
wilcox_test_report

Print Wilcoxon Rank Sum and Signed Rank Tests reprot
theme_zg

A classic theme for ggplot
volcano_plot

Generate Volcano plot base on Deseq_analysis or indicator_analysis results
network_withdiff

Network Analysis with Differential Species
network_visual_re

Re-visualize network plot from network_visual or network_withdiff
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
t_test_report

Print Student's t-Test report
structure_plot

Visualize microbial community composition structure based on tax summary object
Dimension_reduction

Dimension_reduction: PCA, PCOA, and NMDS Analysis
Deseq_analysis

Deseq Analysis Function
Filter_function

Filter OTU/ASV/metagenomic profile/gene profile by threshold
LorMe

LorMe package: Lightening One-Code Resolving Microbial Ecology Program
Facet_group

Tax summary object with Facet 2x2 Groups
Deseq_analysis2

Deseq analysis
Alpha_diversity_calculator2

Calculate alpha diversity based on tax summary object or dataframe table
Module_abundance

Calculate network module abundance for each sample
Module_composition

Pie chart for network module composition
Alpha_diversity_calculator

Calculate alpha diversity based on tax summary object