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 |
Print |
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 |