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LorMe (version 1.1.0)

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

1.1.0

License

GPL-3

Maintainer

Ningqi Wang

Last Published

September 13th, 2024

Functions in LorMe (1.1.0)

circulation_lm

Circulation of fitting Linear Models
NC_remove

Natural connectivity analysis
color_scheme

Get color scheme
community_plot

Generate Community Composition Plot Based on Tax_summary Object
indicator_analysis

Indicator Analysis
manhattan

Manhattan Plot Generator
network_visual

Network Visualization
nc

Calculate Network Natural Connectivity
network_stat

Igraph network statistics
kruskal_report

Print Kruskal-Wallis Rank Sum Test report
compare_plot

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

Generate Differential Bar Plot and Error bar Plot
network_visual_re

Re-visualize network plot from network_visual or network_withdiff
network_withdiff

Network Analysis with Differential Species
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
structure_plot

Visualize microbial community composition structure based on tax summary object
object_config

Set taxonomy summary configuration
t_test_report

Print Student's t-Test report
sub_tax_summary

Subsetting tax summary objects
testotu

test otudata
theme_zg

A classic theme for ggplot
network_analysis2

Conduct Network analysis
tbRDA_analysis

tbRDA analysis
network_analysis

Conduct Network analysis based on tax summary object
tax_summary

Encapsulate meta file, feature tables and taxonomy annotation into tax summary object
Module_abundance

Calculate network module abundance for each sample
Facet_group

Tax summary object with Facet 2x2 Groups
LorMe

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

Pie chart for network module composition
Deseq_analysis

Deseq Analysis Function
Alpha_diversity_calculator2

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

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

Dimension_reduction: PCA, PCOA, and NMDS Analysis
Deseq_analysis2

Deseq analysis
Alpha_diversity_calculator

Calculate alpha diversity based on tax summary object
anova_report

Print Analysis of Variance report
auto_signif_test

Automatic significance test
Three_group

Tax summary object with three groups
Two_group

Tax summary object with two groups
Top_taxa

Calculate top taxa and others
combine_and_translate

Combine data for visualization