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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

0.1.3

License

GPL-3

Issues

0

Pull Requests

0

Stars

19

Forks

2

Maintainer

Peng Chen

Last Published

December 2nd, 2024

Functions in pctax (0.1.3)

convert_taxon_name

Convert taxon names between Chinese and Latin
get_diff_type

Get mean and type
%>%

Pipe operator
multi_bar

Difference analysis
plot.a_res

Plot a_res object
micro_sbatch

Microbiome sbatch
load_N_data

Load N-cycle data
gp_dis_density

Group inter-intra density
nti_rc

Calculate b_NTI and RC_bray for each group
download_taxonkit_dataset

Download taxonkit dataset
pc_otu

Create a pc_otu class object
mat_dist

Calculate distance for otutab
rare_curve_sample

Rare the sample
%<>%

Assignment pipe
taxonkit_list

Taxonkit list
plot_element_cycle

Plot element cycle
envfitt

Envfit test for RDA result
grap_p_test

Performs graph-based permutation tests
plot.b_res

Plot a b_res
taxonkit_lineage

Retrieve Taxonomic Lineage using taxonkit
plot.g_test

Plot g_test
rare_curve_species

Rare the species
cor_net

Correlation network, species-interaction network for omics
diff_da

Difference analysis
name_or_id2df

Transfer taxon name or taxid to the lineage dataframe
df2tree

From a dataframe to construct a phylo
summary.pc_otu

Summary pc_otu
myRDA

RDA
df2tree1

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

Plot two trees in one plot
permanova

Permanova between a otutab and a variable
pctax-package

pctax: Professional Comprehensive Omics Data Analysis
geo_sim

Lm for sample similarity and geographical distance
z_diversity_decay

Calculate Zeta Diversity with Distance
pc_tax1

test data (pc_otu class) for pc_tax package.
install_taxonkit

Install taxonkit
kwtest

KW test
get_all_sp_la_zh_name

get all species Latin and Chinese name from the CCTCC database
z_diversity

Calculate Zeta Diversity
taxonkit_lca

Compute Lowest Common Ancestor (LCA) of TaxIDs
pre_tax_table

Complete a taxonomy table
taxonkit_filter

Filter TaxIDs based on Taxonomic Ranks
pre_fastp

Prepare the result from fastp (.json file)
pc_valid

Judge pc_otu is valid or not
procrustes_analyse

Procrustes Rotation of Two Configurations and PROTEST
print.pc_otu

Print
time_by_cm

Time series analysis
tax_lca

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

Volcano plot for difference analysis
plot_N_cycle

Plot the N-cycling pathway and genes
plot.pro_res

Plot pro_res
ncm

Sloan Neutral Model
nst

Calculate NST for each group
rarefaction

Rarefy a otutab
taxonkit_name2taxid

Convert Taxonomic Names to TaxIDs
suijisenlin

RandomForest
taxonkit_reformat

Reformat Taxonomic Lineage using taxonkit
ann_tree

Annotate a tree
add_strip

add strips for a tree plot
add_tax

Add taxonomy for a pc_otu object
ALDEX

ALDEX
all_ec_info

all element cycle information.
as.b_dist

Transfer dist to b_dist
as.dist.b_dist

Transfer b_dist to dist
aor

Calculate Abundance-occupancy_relationship
RDA_plot

Plot RDA res
all_sp_la_zh_name

all species latin names and chinese names
b_NTI1

Calculate beta_NTI
before_tree

Before df2tree check
b_res_3d

3D plot for b_res
bbtt

ggdotchart for diff analysis
a_diversity

Calculate a_diversity of otutab
plot.time_cm

Plot time_cm
b_analyse

Beta_diversity Ordination: dimensionality reduction
RCbray1

Calculate RCbray-curtis
check_taxonkit

Check taxonkit