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pctax

pctax provides a comprehensive suite of tools for analyzing omics data.

The HTML documentation of the latest version is available at Github page.

Please go to https://bookdown.org/Asa12138/pctax_book/ for the full vignette.

Installation

The stable version is available on CRAN:

install.packages("pctax")

Or you can install the development version of pctax from GitHub with:

# install.packages("devtools")
devtools::install_github("Asa12138/pctax")

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Version

Install

install.packages('pctax')

Monthly Downloads

228

Version

0.1.7

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/Asa12138/pctax

Maintainer

Chen Peng

Last Published

February 9th, 2026

Functions in pctax (0.1.7)

From a dataframe to construct a phylo (save nwk)

Transfer b_dist to dist

Envfit test for RDA result

drop_tips_update

Drop Tips and Update a Phylogenetic Tree

From a dataframe to construct a phylo

ggdotchart for diff analysis

Assignment pipe

Performs graph-based permutation tests

Difference analysis

Before df2tree check

download_taxonkit_dataset

Download taxonkit dataset

install_taxonkit

Install taxonkit

Calculate beta_NTI

Beta_diversity Ordination: dimensionality reduction

Load a metaphlan format data.frame

Load N-cycle data

Transfer taxon name or taxid to the lineage dataframe

Group inter-intra density

Plot a_res object

Get mean and type

Calculate NST for each group

pctax: Professional Comprehensive Omics Data Analysis

convert_taxon_name

Convert taxon names between Chinese and Latin

Sloan Neutral Model

Permanova between a otutab and a variable

Difference analysis

procrustes_analyse

Procrustes Rotation of Two Configurations and PROTEST

rare_curve_sample

Rare the sample

Correlation network, species-interaction network for omics

Microbiome sbatch

Calculate distance for otutab

Lm for sample similarity and geographical distance

get_all_sp_la_zh_name

get all species Latin and Chinese name from the CCTCC database

Plot two trees in one plot

Plot Individual Phage Genome Structure with Annotations

test data (pc_otu class) for pc_tax package.

pre_format_report

Preprocess MPA Species Abundance and Taxonomy Data

Judge pc_otu is valid or not

pre_assembly_stats

Prepare the result from assembly_stats (.json file)

Plot the N-cycling pathway and genes

Prepare the result from fastp (.json file)

Stamp style plot

Time series analysis

Create a pc_otu class object

Calculate b_NTI and RC_bray for each group

Preprocess geNomad and CheckV Output Results

Volcano plot for difference analysis

taxonkit_reformat

Reformat Taxonomic Lineage using taxonkit

taxonkit_name2taxid

Convert Taxonomic Names to TaxIDs

taxonkit_lineage

Retrieve Taxonomic Lineage using taxonkit

Calculate the lowest common ancestor (LCA) of a set of taxa

rare_curve_species

Rare the species

Preprocess GTDB-Tk Classification Results

z_diversity_decay

Calculate Zeta Diversity with Distance

Complete a taxonomy table

Calculate Zeta Diversity

Rarefy a otutab

plot_element_cycle

Plot element cycle

plot_contigs_quality

Visualize Contigs Quality Metrics

plot_checkm2_res

Visualize CheckM2 Genome Quality Assessment Results

Plot GTDB-Tk Phylogenetic Tree with Taxonomic Coloring

Difference analysis

taxonkit_filter

Filter TaxIDs based on Taxonomic Ranks

print.virus_res

Print method for virus_res objects

Compute Lowest Common Ancestor (LCA) of TaxIDs

Annotate a tree

add strips for a tree plot

all_sp_la_zh_name

all species latin names and chinese names

Add taxonomy for a pc_otu object

Calculate RCbray-curtis

Calculate a_diversity of otutab

all element cycle information.

Calculate Abundance-occupancy_relationship

Transfer dist to b_dist

3D plot for b_res