Package: pctax 0.1.3

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]

pctax_0.1.3.tar.gz
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pctax.pdf |pctax.html✨
pctax/json (API)
NEWS

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

Peer review:

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

Datasets:
  • all_ec_info - All element cycle information.
  • pc_tax1 - Test data (pc_otu class) for pc_tax package.

On CRAN:

microbiomesoftwarevisualizationomics

5.69 score 9 stars 11 scripts 138 downloads 70 exports 79 dependencies

Last updated 14 days agofrom:11e21a768d. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 23 2024
R-4.5-winERROROct 23 2024
R-4.5-linuxERROROct 23 2024
R-4.4-winERROROct 23 2024
R-4.4-macERROROct 23 2024
R-4.3-winERROROct 23 2024
R-4.3-macERROROct 23 2024

Exports:%<>%%>%a_diversityadd_stripadd_taxALDEXann_treeaoras.b_distb_analyseb_NTI1b_res_3dbbttbefore_treecheck_taxonkitcor_netdf2treedf2tree1diff_dadownload_taxonkit_dataseteasy_treeenvfittgene2idgeo_simget_diff_typegp_dis_densitygrap_p_testinstall_taxonkitkwtestload_N_datam_group_envmat_distmicro_sbatchmulti_barmyCAPmyCCAmyRDAname_or_id2dfncmnstnti_rcpc_otupc_validpermanovaplot_element_cycleplot_N_cycleplot_two_treepre_fastppre_GEOpre_tax_tableprocrustes_analyserare_curve_samplerare_curve_speciesrarefactionRCbray1RDA_plotsangji_plotsuijisenlinsunbursttax_lcataxonkit_filtertaxonkit_lcataxonkit_lineagetaxonkit_listtaxonkit_name2taxidtaxonkit_reformattime_by_cmvolcano_pz_diversityz_diversity_decay

Dependencies:abindade4backportsbootbroomcarcarDatacliclustercolorspacecorrplotcowplotcpp11DerivdoBydplyrfansifarverFormulagenericsggnewscaleggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpcutilspermutepillarpixmappkgconfigplyrpolynompurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangrstatixscalesspSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsveganviridisLitewithr

Quick start: pctax

Rendered frompctax.Rmdusingknitr::rmarkdownon Oct 23 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Calculate a_diversity of otutaba_diversity a_diversity.data.frame a_diversity.numeric a_diversity.pc_otu
add strips for a tree plotadd_strip
Add taxonomy for a pc_otu objectadd_tax
ALDEXALDEX
all element cycle information.all_ec_info
Annotate a treeann_tree easy_tree
Calculate Abundance-occupancy_relationshipaor aor.data.frame plot.AOR
Transfer dist to b_distas.b_dist plot.b_dist plot.dist
Transfer b_dist to distas.dist.b_dist
Beta_diversity Ordination: dimensionality reductionb_analyse b_analyse.data.frame
Calculate beta_NTIb_NTI1
3D plot for b_resb_res_3d
ggdotchart for diff analysisbbtt
Before df2tree checkbefore_tree
Check taxonkitcheck_taxonkit
Correlation network, species-interaction network for omicscor_net
From a dataframe to construct a phylodf2tree
From a dataframe to construct a phylo (save nwk)df2tree1
Difference analysisdiff_da
Download taxonkit datasetdownload_taxonkit_dataset
Envfit test for RDA resultenvfitt
Gene symbolid transfer to entrezIDs (human gene)gene2id
Lm for sample similarity and geographical distancegeo_sim
Get mean and typeget_diff_type
Group inter-intra densitygp_dis_density
Performs graph-based permutation testsgrap_p_test
Install taxonkitinstall_taxonkit
KW testkwtest
Load N-cycle dataload_N_data
Multi-table test with envm_group_env plot.mant_g
Calculate distance for otutabmat_dist
Microbiome sbatchmicro_sbatch
Difference analysismulti_bar
RDAmyCAP myCCA myRDA
Transfer taxon name or taxid to the lineage dataframename_or_id2df
Sloan Neutral Modelncm plot.ncm_res
Calculate NST for each groupnst
Calculate b_NTI and RC_bray for each groupnti_rc plot.NTI_RC
Create a pc_otu class objectpc_otu
test data (pc_otu class) for pc_tax package.pc_tax1
Judge pc_otu is valid or notpc_valid
Permanova between a otutab and a variablepermanova
Plot element cycleplot_element_cycle
Plot the N-cycling pathway and genesplot_N_cycle
Plot two trees in one plotplot_two_tree
Plot a_res objectplot.a_res
Plot a b_resplot.b_res
Plot g_testplot.g_test
Plot pro_resplot.pro_res
Plot time_cmplot.time_cm
Prepare the result from fastp (.json file)pre_fastp
prepare the GEO datapre_GEO
Complete a taxonomy tablepre_tax_table
Printprint.pc_otu
Procrustes Rotation of Two Configurations and PROTESTprocrustes_analyse
Rare the sampleplot.rare_res rare_curve_sample
Rare the speciesrare_curve_species
Rarefy a otutabrarefaction
Calculate RCbray-curtisRCbray1
Plot RDA resRDA_plot
Plot a sankeysangji_plot
RandomForestsuijisenlin
Summary pc_otusummary.pc_otu
Plot a sunburstsunburst
Calculate the lowest common ancestor (LCA) of a set of taxatax_lca
Filter TaxIDs based on Taxonomic Rankstaxonkit_filter
Compute Lowest Common Ancestor (LCA) of TaxIDstaxonkit_lca
Retrieve Taxonomic Lineage using taxonkittaxonkit_lineage
Taxonkit listtaxonkit_list
Convert Taxonomic Names to TaxIDstaxonkit_name2taxid
Reformat Taxonomic Lineage using taxonkittaxonkit_reformat
Time series analysistime_by_cm
Volcano plot for difference analysisvolcano_p
Calculate Zeta Diversityplot.zeta_res z_diversity
Calculate Zeta Diversity with Distanceplot.zeta_decay z_diversity_decay