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LorMe (version 2.0.1)

Lightweight One-Line Resolving Microbial Ecology Program

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

359

Version

2.0.1

License

GPL-3

Maintainer

Ningqi Wang

Last Published

November 17th, 2025

Functions in LorMe (2.0.1)

color_scheme

Get color scheme
auto_signif_test

Automatic significance test
community_plot

Generate Community Composition Plot Based on Tax_summary Object
Trans_to_phylo

Convert a LorMe object to a phyloseq object
Two_group

Tax summary object with two groups
anova_report

Print Analysis of Variance report
combine_and_translate

Combine data for visualization
add_tree

Attach phylogenetic tree to the LorMe object
circulation_lm

Circulation of fitting Linear Models
$,LorMe-method

Access LorMe object elements via $
nc

Calculate Network Natural Connectivity
network_analysis

Conduct Network analysis based on tax summary object
.onLoad

Accessed by getOption("LorMe") or LorMe_options()
manhattan

Manhattan Plot Generator
.DollarNames.LorMe

Tab completion for LorMe $ access
compare_plot

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

Print Kruskal-Wallis Rank Sum Test report
differential_bar

Generate Differential Bar Plot and Error bar Plot
indicator_analysis

Indicator Analysis
.LorMe_opts

Global options for LorMe pipeline analysis
network_withdiff

Network Analysis with Differential Species
show,LorMe-method

Show method for LorMe objects
object_config

Set taxonomy summary configuration
network_visual_re

Re-visualize network plot from network_visual or network_withdiff
structure_plot

Visualize microbial community composition structure based on tax summary object
network_visual

Network Visualization
safe_run

Running function with safe mode
network_stat

Igraph network statistics
network_analysis2

Conduct Network analysis
sub_tax_summary

Subsetting tax summary objects
volcano_plot

Generate Volcano plot base on Deseq_analysis or indicator_analysis results
theme_zg

A classic theme for ggplot
testotu

test otudata
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
wilcox_test_report

Print Wilcoxon Rank Sum and Signed Rank Tests reprot
Alpha_diversity_calculator2

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

Calculate alpha diversity based on tax summary object
LorMe-package

LorMe: Lightweight One-Line Resolving Microbial Ecology Program
Deseq_analysis

Deseq Analysis Function
Deseq_analysis2

Deseq analysis
Filter_function

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

Tax summary object with Facet 2x2 Groups
Dimension_reduction

Dimension_reduction: PCA, PCOA, and NMDS Analysis
LorMe-class

LorMe S4 class
Module_composition

Pie chart for network module composition
Module_abundance

Calculate network module abundance for each sample
LorMe_defaults

Restore LorMe global options to factory defaults
Trans_to_microeco

Convert a LorMe object to a microeco object
Trans_from_phylo

Convert phyloseq object to LorMe object
Top_taxa

Calculate top taxa and others
NC_remove

Natural connectivity analysis
LorMe_options

Change LorMe options
Trans_from_microeco

Convert a microeco object to a LorMe object
Three_group

Tax summary object with three groups
LorMe_pipeline

One-stop microbial analysis pipeline for LorMe objects