Package: pctax 0.1.8

Chen Peng

pctax: Professional Comprehensive Omics Data Analysis

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.

Authors:Chen Peng [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pctax/json (API)

# Install 'pctax' in R:

install.packages('pctax', repos = c('https://asa12138.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/asa12138/pctax/issues

Datasets:

all_ec_info - All element cycle information.
all_sp_la_zh_name - All species latin names and chinese names
pc_tax1 - Test data (pc_otu class) for pc_tax package.

On CRAN:

microbiome software visualization omics

5.94 score 32 stars 18 scripts 299 downloads 85 exports 98 dependencies

Last updated from:266e7db607. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	303
source / vignettes	OK	420
linux-release-x86_64	NOTE	323
macos-release-arm64	NOTE	186
macos-oldrel-arm64	NOTE	187
windows-devel	NOTE	237
windows-release	NOTE	204
windows-oldrel	NOTE	261
wasm-release	OK	274

Exports:%<>%%>%a_diversity add_strip add_tax ALDEX ann_tree aor as.b_dist b_analyse b_NTI1 b_res_3d batch_mediate bbtt before_tree check_taxonkit convert_taxon_name cor_net df2tree df2tree1 diff_da download_taxonkit_dataset drop_tips_update easy_tree envfitt gene2id geo_sim get_diff_type gp_dis_density grap_p_test install_taxonkit kwtest load_mpa_df load_N_data m_group_env mat_dist micro_sbatch multi_bar multi_conf myCAP myCCA myRDA name_or_id2df ncm nst nti_rc pc_otu pc_valid permanova plot_checkm2_res plot_contigs_quality plot_element_cycle plot_gtdb_tr plot_N_cycle plot_one_phage plot_two_tree pre_assembly_stats pre_fastp pre_format_report pre_genomad pre_GEO pre_gtdb_tk pre_tax_table procrustes_analyse rare_curve_sample rare_curve_species rarefaction RCbray1 RDA_plot sangji_plot stamp_plot suijisenlin sunburst tax_lca taxonkit_filter taxonkit_lca taxonkit_lineage taxonkit_list taxonkit_name2taxid taxonkit_reformat taxonkit_reformat2 time_by_cm volcano_p z_diversity z_diversity_decay

Dependencies:abind ade4 backports bit bit64 boot broom car carData cli clipr cluster colorspace corrplot cowplot cpp11 crayon Deriv doBy dplyr farver forecast Formula fracdiff generics ggnewscale ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable hms isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa modelr nlme nloptr nnet numDeriv patchwork pbkrtest pcutils permute pillar pixmap pkgconfig plyr polynom prettyunits progress purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas reshape2 rlang rstatix S7 scales sp SparseM stringi stringr survival tibble tidyr tidyselect timeDate tzdb urca utf8 vctrs vegan viridisLite vroom withr zoo

Quick start: pctax

pctax | Vignette | Install | Usage | Citation

Rendered frompctax.Rmdusingknitr::rmarkdown

Last update: 2024-04-06
Started: 2023-06-20

Help page	Topics
Calculate a_diversity of otutab	a_diversity a_diversity.data.frame a_diversity.numeric a_diversity.pc_otu
add strips for a tree plot	add_strip
Add taxonomy for a pc_otu object	add_tax
ALDEX	ALDEX
all element cycle information.	all_ec_info
all species latin names and chinese names	all_sp_la_zh_name
Annotate a tree	ann_tree easy_tree
Calculate Abundance-occupancy_relationship	aor aor.data.frame plot.AOR
Transfer dist to b_dist	as.b_dist plot.b_dist plot.dist
Transfer b_dist to dist	as.dist.b_dist
Beta_diversity Ordination: dimensionality reduction	b_analyse b_analyse.data.frame
Calculate beta_NTI	b_NTI1
3D plot for b_res	b_res_3d
Batch mediate	batch_mediate
ggdotchart for diff analysis	bbtt
Before df2tree check	before_tree
Check taxonkit	check_taxonkit
Convert taxon names between Chinese and Latin	convert_taxon_name
Correlation network, species-interaction network for omics	cor_net
From a dataframe to construct a phylo	df2tree
From a dataframe to construct a phylo (save nwk)	df2tree1
Difference analysis	diff_da
Download taxonkit dataset	download_taxonkit_dataset
Drop Tips and Update a Phylogenetic Tree	drop_tips_update
Envfit test for RDA result	envfitt
Gene symbolid transfer to entrezIDs (human gene)	gene2id
Lm for sample similarity and geographical distance	geo_sim
get all species Latin and Chinese name from the CCTCC database	get_all_sp_la_zh_name
Get mean and type	get_diff_type
Group inter-intra density	gp_dis_density
Performs graph-based permutation tests	grap_p_test
Install taxonkit	install_taxonkit
KW test	kwtest
Load a metaphlan format data.frame	load_mpa_df
Load N-cycle data	load_N_data
Multi-table test with env	m_group_env plot.mant_g
Calculate distance for otutab	mat_dist
Microbiome sbatch	micro_sbatch
Difference analysis	multi_bar
Difference analysis	multi_conf
RDA	myCAP myCCA mydbRDA myRDA
Transfer taxon name or taxid to the lineage dataframe	name_or_id2df
Sloan Neutral Model	ncm plot.ncm_res
Calculate NST for each group	nst
Calculate b_NTI and RC_bray for each group	nti_rc plot.NTI_RC
Create a pc_otu class object	pc_otu
test data (pc_otu class) for pc_tax package.	pc_tax1
Judge pc_otu is valid or not	pc_valid
Permanova between a otutab and a variable	permanova
Permanova between a otutab and a variable (added 'two')	permanova2
Visualize CheckM2 Genome Quality Assessment Results	plot_checkm2_res
Visualize Contigs Quality Metrics	plot_contigs_quality
Plot element cycle	plot_element_cycle
Plot GTDB-Tk Phylogenetic Tree with Taxonomic Coloring	plot_gtdb_tr
Plot the N-cycling pathway and genes	plot_N_cycle
Plot Individual Phage Genome Structure with Annotations	plot_one_phage
Plot two trees in one plot	plot_two_tree
Plot a_res object	plot.a_res
Plot a b_res	plot.b_res
Plot g_test	plot.g_test
Plot pro_res	plot.pro_res
Plot time_cm	plot.time_cm
Prepare the result from assembly_stats (.json file)	pre_assembly_stats
Prepare the result from fastp (.json file)	pre_fastp
Preprocess MPA Species Abundance and Taxonomy Data	pre_format_report
Preprocess geNomad and CheckV Output Results	pre_genomad
prepare the GEO data	pre_GEO
Preprocess GTDB-Tk Classification Results	pre_gtdb_tk
Complete a taxonomy table	pre_tax_table
Print	print.pc_otu
Print method for virus_res objects	print.virus_res
Procrustes Rotation of Two Configurations and PROTEST	procrustes_analyse
Rare the sample	plot.rare_res rare_curve_sample
Rare the species	rare_curve_species
Rarefy a otutab	rarefaction
Calculate RCbray-curtis	RCbray1
Plot RDA res	RDA_plot
Plot a sankey	sangji_plot
Stamp style plot	stamp_plot
RandomForest	suijisenlin
Summary pc_otu	summary.pc_otu
Plot a sunburst	sunburst
Calculate the lowest common ancestor (LCA) of a set of taxa	tax_lca
Filter TaxIDs based on Taxonomic Ranks	taxonkit_filter
Compute Lowest Common Ancestor (LCA) of TaxIDs	taxonkit_lca
Retrieve Taxonomic Lineage using taxonkit	taxonkit_lineage
Taxonkit list	taxonkit_list
Convert Taxonomic Names to TaxIDs	taxonkit_name2taxid
Reformat Taxonomic Lineage using taxonkit	taxonkit_reformat
Reformat Taxonomic Lineage using taxonkit reformat2	taxonkit_reformat2
Time series analysis	time_by_cm
Volcano plot for difference analysis	volcano_p
Calculate Zeta Diversity	plot.zeta_res z_diversity
Calculate Zeta Diversity with Distance	plot.zeta_decay z_diversity_decay

Package: pctax 0.1.8

pctax: Professional Comprehensive Omics Data Analysis

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Help Manual

Usage by other packages (reverse dependencies)