Lightweight One-Line Resolving Microbial Ecology Program
Attach phylogenetic tree to the LorMe object
Calculate alpha diversity based on tax summary object
Calculate alpha diversity based on tax summary object or dataframe tab...
Print Analysis of Variance report
Automatic significance test
Access LorMe object elements via $
Circulation of fitting Linear Models
Get color scheme
Combine data for visualization
Generate Community Composition Plot Based on Tax_summary Object
Comparison plot generator This function help generate comparsion plot ...
Deseq Analysis Function
Deseq analysis
Generate Differential Bar Plot and Error bar Plot
Dimension_reduction: PCA, PCOA, and NMDS Analysis
Tab completion for LorMe $ access
Global options for LorMe pipeline analysis
Accessed by getOption("LorMe") or LorMe_options()
Filter OTU/ASV/metagenomic profile/gene profile by threshold
Indicator Analysis
Print Kruskal-Wallis Rank Sum Test report
Restore LorMe global options to factory defaults
Change LorMe options
One-stop microbial analysis pipeline for LorMe objects
LorMe S4 class
LorMe: Lightweight One-Line Resolving Microbial Ecology Program
Manhattan Plot Generator
Calculate network module abundance for each sample
Pie chart for network module composition
Natural connectivity analysis
Calculate Network Natural Connectivity
Conduct Network analysis based on tax summary object
Conduct Network analysis
Igraph network statistics
Re-visualize network plot from network_visual or network_withdiff
Network Visualization
Network Analysis with Differential Species
Set taxonomy summary configuration
Running function with safe mode
Show method for LorMe objects
Visualize microbial community composition structure based on tax summa...
Subsetting tax summary objects
Print Student's t-Test report
Encapsulate meta file, feature tables and taxonomy annotation into tax...
tbRDA analysis
A classic theme for ggplot
Calculate top taxa and others
Convert a microeco object to a LorMe object
Convert phyloseq object to LorMe object
Convert a LorMe object to a microeco object
Convert a LorMe object to a phyloseq object
Generate Volcano plot base on Deseq_analysis or indicator_analysis res...
Print Wilcoxon Rank Sum and Signed Rank Tests reprot
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.