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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

149

Version

0.1.1

License

GPL-3

Issues

0

Pull Requests

0

Stars

19

Forks

2

Maintainer

Peng Chen

Last Published

December 2nd, 2024

Functions in pctax (0.1.1)

%<>%

Assignment pipe
install_taxonkit

Install taxonkit
cor_net

Correlation network, species-interaction network for omics
kwtest

KW test
diff_da

Difference analysis
nst

Calculate NST for each group
name_or_id2df

Transfer taxon name or taxid to the lineage dataframe
ncm

Sloan Neutral Model
before_tree

Before df2tree check
bbtt

ggdotchart for diff analysis
df2tree1

From a dataframe to construct a phylo (save nwk)
nti_rc

Calculate b_NTI and RC_bray for each group
gp_dis_density

Group inter-intra density
get_diff_type

Get mean and type
df2tree

From a dataframe to construct a phylo
permanova

Permanova between a otutab and a variable
download_taxonkit_dataset

Download taxonkit dataset
pctax-package

pctax: Professional Comprehensive Omics Data Analysis
envfitt

Envfit test for RDA result
pc_valid

Judge pc_otu is valid or not
geo_sim

Lm for sample similarity and geographical distance
plot_N_cycle

Plot the N-cycling pathway and genes
load_N_data

Load N-cycle data
%>%

Pipe operator
mat_dist

Calculate distance for otutab
plot_element_cycle

Plot element cycle
plot.a_res

Plot a_res object
pre_fastp

Prepare the result from fastp (.json file)
micro_sbatch

Microbiome sbatch
plot.pro_res

Plot pro_res
plot.g_test

Plot g_test
print.pc_otu

Print
pre_tax_table

Complete a taxonomy table
procrustes_analyse

Procrustes Rotation of Two Configurations and PROTEST
taxonkit_name2taxid

Convert Taxonomic Names to TaxIDs
taxonkit_list

Taxonkit list
myRDA

RDA
pc_otu

Create a pc_otu class object
multi_bar

Difference analysis
grap_p_test

Performs graph-based permutation tests
pc_tax1

test data (pc_otu class) for pc_tax package.
rarefaction

Rarefy a otutab
suijisenlin

RandomForest
plot.b_res

Plot a b_res
taxonkit_filter

Filter TaxIDs based on Taxonomic Ranks
summary.pc_otu

Summary pc_otu
z_diversity_decay

Calculate Zeta Diversity with Distance
rare_curve_sample

Rare the sample
rare_curve_species

Rare the species
taxonkit_reformat

Reformat Taxonomic Lineage using taxonkit
time_by_cm

Time series analysis
taxonkit_lca

Compute Lowest Common Ancestor (LCA) of TaxIDs
taxonkit_lineage

Retrieve Taxonomic Lineage using taxonkit
volcano_p

Volcano plot for difference analysis
z_diversity

Calculate Zeta Diversity
RDA_plot

Plot RDA res
add_strip

add strips for a tree plot
aor

Calculate Abundance-occupancy_relationship
all_ec_info

all element cycle information.
a_diversity

Calculate a_diversity of otutab
ann_tree

Annotate a tree
as.b_dist

Transfer dist to b_dist
add_tax

Add taxonomy for a pc_otu object
ALDEX

ALDEX
RCbray1

Calculate RCbray-curtis
check_taxonkit

Check taxonkit
plot.time_cm

Plot time_cm
as.dist.b_dist

Transfer b_dist to dist
b_NTI1

Calculate beta_NTI
b_analyse

Beta_diversity Ordination: dimensionality reduction
b_res_3d

3D plot for b_res