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. |
ann_tree | Annotate a tree |
aor | Calculate Abundance-occupancy_relationship |
aor.data.frame | Calculate Abundance-occupancy_relationship |
as.b_dist | Transfer dist to b_dist |
as.dist.b_dist | Transfer b_dist to dist |
a_diversity | Calculate a_diversity of otutab |
a_diversity.data.frame | Calculate a_diversity of otutab |
a_diversity.numeric | Calculate a_diversity of otutab |
a_diversity.pc_otu | Calculate a_diversity of otutab |
bbtt | ggdotchart for diff analysis |
before_tree | Before df2tree check |
b_analyse | Beta_diversity Ordination: dimensionality reduction |
b_analyse.data.frame | Beta_diversity Ordination: dimensionality reduction |
b_NTI1 | Calculate beta_NTI |
b_res_3d | 3D plot for b_res |
check_taxonkit | Check taxonkit |
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 |
easy_tree | Annotate a tree |
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 |
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 |
myCAP | RDA |
myCCA | RDA |
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. |
pc_valid | Judge pc_otu is valid or not |
permanova | Permanova between a otutab and a variable |
plot.AOR | Calculate Abundance-occupancy_relationship |
plot.a_res | Plot a_res object |
plot.b_dist | Transfer dist to b_dist |
plot.b_res | Plot a b_res |
plot.dist | Transfer dist to b_dist |
plot.g_test | Plot g_test |
plot.ncm_res | Sloan Neutral Model |
plot.NTI_RC | Calculate b_NTI and RC_bray for each group |
plot.pro_res | Plot pro_res |
plot.rare_res | Rare the sample |
plot.time_cm | Plot time_cm |
plot.zeta_decay | Calculate Zeta Diversity with Distance |
plot.zeta_res | Calculate Zeta Diversity |
plot_element_cycle | Plot element cycle |
plot_N_cycle | Plot the N-cycling pathway and genes |
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 |
rarefaction | Rarefy a otutab |
rare_curve_sample | Rare the sample |
rare_curve_species | Rare the species |
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 |