Professional Comprehensive Omics Data Analysis


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Documentation for package ‘pctax’ version 0.1.1

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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