Professional Comprehensive Omics Data Analysis
Calculate a_diversity of otutab
add strips for a tree plot
Add taxonomy for a pc_otu object
ALDEX
Annotate a tree
Calculate Abundance-occupancy_relationship
Transfer dist to b_dist
Transfer b_dist to dist
Beta_diversity Ordination: dimensionality reduction
Calculate beta_NTI
3D plot for b_res
ggdotchart for diff analysis
Before df2tree check
Plot time_cm
Check taxonkit
Convert taxon names between Chinese and Latin
Correlation network, species-interaction network for omics
From a dataframe to construct a phylo
From a dataframe to construct a phylo (save nwk)
Difference analysis
Download taxonkit dataset
Envfit test for RDA result
Lm for sample similarity and geographical distance
get all species Latin and Chinese name from the CCTCC database
Get mean and type
Group inter-intra density
Performs graph-based permutation tests
Assignment pipe
Install taxonkit
KW test
Load N-cycle data
Calculate distance for otutab
Microbiome sbatch
Difference analysis
RDA
Transfer taxon name or taxid to the lineage dataframe
Sloan Neutral Model
Calculate NST for each group
Calculate b_NTI and RC_bray for each group
Create a pc_otu class object
Judge pc_otu is valid or not
pctax: Professional Comprehensive Omics Data Analysis
Permanova between a otutab and a variable
Pipe operator
Plot element cycle
Plot the N-cycling pathway and genes
Plot two trees in one plot
Plot a_res object
Plot a b_res
Plot g_test
Plot pro_res
Prepare the result from fastp (.json file)
Complete a taxonomy table
Procrustes Rotation of Two Configurations and PROTEST
Rare the sample
Rare the species
Rarefy a otutab
Calculate RCbray-curtis
Plot RDA res
RandomForest
Summary pc_otu
Calculate the lowest common ancestor (LCA) of a set of taxa
Filter TaxIDs based on Taxonomic Ranks
Compute Lowest Common Ancestor (LCA) of TaxIDs
Retrieve Taxonomic Lineage using taxonkit
Taxonkit list
Convert Taxonomic Names to TaxIDs
Reformat Taxonomic Lineage using taxonkit
Time series analysis
Volcano plot for difference analysis
Calculate Zeta Diversity with Distance
Calculate Zeta Diversity
Provides a comprehensive suite of tools for analyzing omics data. It includes functionalities for alpha diversity analysis, beta diversity analysis, differential abundance analysis, community assembly analysis, visualization of phylogenetic tree, and functional enrichment analysis. With a progressive approach, the package offers a range of analysis methods to explore and understand the complex communities. It is designed to support researchers and practitioners in conducting in-depth and professional omics data analysis.