pctax

0.1.7

Professional Comprehensive Omics Data Analysis

0packages depend

15Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Chen PengFirst published 2024-02-274 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("pctax", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("Asa12138/pctax")

Development version from Asa12138/pctax. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-pctax

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-pctax

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-pctax

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.9 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

97%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 200 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 66%
Documented parameters: 98%
Return-value docs: 100%
References docs: 10%

Downloads

15K

CRAN downloads in the past year

Rank #13,246 · ~41/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

23030 days

81590 days

15K1 year

Compare downloads with other packages →

Also on111 r2u17 autocran

Repository

GitHub ↗ asa12138/pctax

32Stars

4Forks

0Open issues

1Open PRs

0Releases

69Commits

2Contributors

microbiomeromics

69 commits · Last activity 2026-04-03 · 0% stars, 30d

Stars over time

2025-07-03 · 232026-07-07 · 32

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/asa12138/pctax on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

61 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (18)

pcutils dplyr readr ggplot2 vegan magrittrgrDevicesRColorBrewer ggrepel reshape2statstibbleutilsggpubr patchwork ggnewscale ade4 scales

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Chen Peng

Author, Maintainer

Authors (1)

Chen Peng

Author, Maintainer

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.7Latest
2026-02-09 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.3
2024-12-02 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.1
2024-04-10 · diff ↗
unarchivedReturned to CRAN
2024-04-10
archivedRemoved from CRAN
2024-03-10
requires archived package 'pcutils'
0.1.0
2024-02-27
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-27
Total releases: 4 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2.0
Bundled data: 419 KB / 3 files
Download size: 1.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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