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pctax

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

Install

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

🚀 NEWS 🚀

Recently I added a function to plot element cycling because element cycling genes are important in the microbiome (especially the environmental microbiome). Supports simple cycle diagram drawing of C, N, P, S, Fe (manual arrangement, there must be some missing parts, will be continuously added in the future):

plot_element_cycle(cycle = "Nitrogen cycle")
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the pctax package.
#>   Please report the issue at <https://github.com/Asa12138/pctax/issues>.
#> recommend ggsave(width = 12,height = 10)

Usage

For the full vignette, please visit pctax: Analyzing Omics Data with R.

Some Functionalities of pctax:

flowchart LR
  B(pctax)--> C{Functionalities}
  C --> D[Visualization]
  C --> E[Diversity Analysis]
  C --> F[Differential Abundance Analysis]
  C --> G[Community Assembly Analysis]
  C --> H[Functional Enrichment Analysis]
  C --> I[Network Analysis]
  C --> J[Elemental Cycling Analysis]

Citation

Please cite:

Chen Peng, Chao Jiang (2023). pctax: Professional Comprehensive Microbiome Data Analysis Pipeline. R package, https://github.com/Asa12138/pctax.