Man pages for pctax
Professional Comprehensive Omics Data Analysis
| add_strip | add strips for a tree plot |
| add_tax | Add taxonomy for a pc_otu object |
| a_diversity | Calculate a_diversity of otutab |
| ALDEX | ALDEX |
| all_ec_info | all element cycle information. |
| ann_tree | Annotate a tree |
| aor | Calculate Abundance-occupancy_relationship |
| as.b_dist | Transfer dist to b_dist |
| as.dist.b_dist | Transfer b_dist to dist |
| b_analyse | Beta_diversity Ordination: dimensionality reduction |
| bbtt | ggdotchart for diff analysis |
| before_tree | Before df2tree check |
| b_NTI1 | Calculate beta_NTI |
| b_res_3d | 3D plot for b_res |
| check_taxonkit | Check taxonkit |
| c_means | Plot time_cm |
| cor_net | Correlation network, species-interaction network for omics |
| df2tree | From a dataframe to construct a phylo |
| df2tree1 | From a dataframe to construct a phylo (save nwk) |
| diff_da | Difference analysis |
| download_taxonkit_dataset | Download taxonkit dataset |
| envfitt | Envfit test for RDA result |
| geo_sim | Lm for sample similarity and geographical distance |
| get_diff_type | Get mean and type |
| gp_dis_density | Group inter-intra density |
| grapes-less-than-greater-than-grapes | Assignment pipe |
| grap_p_test | Performs graph-based permutation tests |
| install_taxonkit | Install taxonkit |
| kwtest | KW test |
| load_N_data | Load N-cycle data |
| mat_dist | Calculate distance for otutab |
| micro_sbatch | Microbiome sbatch |
| multi_bar | Difference analysis |
| myRDA | RDA |
| name_or_id2df | Transfer taxon name or taxid to the lineage dataframe |
| ncm | Sloan Neutral Model |
| nst | Calculate NST for each group |
| nti_rc | Calculate b_NTI and RC_bray for each group |
| pc_otu | Create a pc_otu class object |
| pc_tax1 | test data (pc_otu class) for pc_tax package. |
| pctax-package | pctax: Professional Comprehensive Omics Data Analysis |
| pc_valid | Judge pc_otu is valid or not |
| permanova | Permanova between a otutab and a variable |
| pipe | Pipe operator |
| plot.a_res | Plot a_res object |
| plot.b_res | Plot a b_res |
| plot_element_cycle | Plot element cycle |
| plot.g_test | Plot g_test |
| plot_N_cycle | Plot the N-cycling pathway and genes |
| plot.pro_res | Plot pro_res |
| pre_fastp | Prepare the result from fastp (.json file) |
| pre_tax_table | Complete a taxonomy table |
| print.pc_otu | |
| procrustes_analyse | Procrustes Rotation of Two Configurations and PROTEST |
| rare_curve_sample | Rare the sample |
| rare_curve_species | Rare the species |
| rarefaction | Rarefy a otutab |
| RCbray1 | Calculate RCbray-curtis |
| RDA_plot | Plot RDA res |
| suijisenlin | RandomForest |
| summary.pc_otu | Summary pc_otu |
| taxonkit_filter | Filter TaxIDs based on Taxonomic Ranks |
| taxonkit_lca | Compute Lowest Common Ancestor (LCA) of TaxIDs |
| taxonkit_lineage | Retrieve Taxonomic Lineage using taxonkit |
| taxonkit_list | Taxonkit list |
| taxonkit_name2taxid | Convert Taxonomic Names to TaxIDs |
| taxonkit_reformat | Reformat Taxonomic Lineage using taxonkit |
| time_by_cm | Time series analysis |
| volcano_p | Volcano plot for difference analysis |
| z_diversity | Calculate Zeta Diversity |
| z_diversity_decay | Calculate Zeta Diversity with Distance |
