Man pages for microeco
Microbial Community Ecology Data Analysis
| clone | Copy an R6 class object |
| dataset | The dataset structured with microtable class for the... |
| dropallfactors | Remove all factors in a data frame |
| env_data_16S | The environmental factors for the 16S example data |
| fungi_func_FungalTraits | The FungalTraits database for fungi trait prediction |
| fungi_func_FUNGuild | The FUNGuild database for fungi trait prediction |
| microeco | Introduction to microeco package... |
| microtable | Create 'microtable' object to store and manage all the basic... |
| otu_table_16S | The OTU table of the 16S example data |
| otu_table_ITS | The OTU table of the ITS example data |
| phylo_tree_16S | The phylogenetic tree of 16S example data |
| prok_func_FAPROTAX | Customized FAPROTAX trait database |
| prok_func_NJC19_list | The NJC19 database |
| sample_info_16S | The sample information of 16S example data |
| sample_info_ITS | The sample information of ITS example data |
| soil_metab | Microtable object of non-targeted metabolome data from bulk... |
| soil_microb | Microtable object of prokaryotic sequencing data from soil... |
| Tax4Fun2_KEGG | The KEGG data files used in the trans_func class |
| taxonomy_table_16S | The taxonomic information of 16S example data |
| taxonomy_table_ITS | The taxonomic information of ITS example data |
| tidy_taxonomy | Clean up the taxonomic table to make taxonomic assignments... |
| trans_abund | Create 'trans_abund' object for taxonomic abundance... |
| trans_alpha | Create 'trans_alpha' object for alpha diversity statistics... |
| trans_beta | Create 'trans_beta' object for beta-diversity analysis |
| trans_classifier | Create 'trans_classifier' object for machine-learning-based... |
| trans_diff | Create 'trans_diff' object for the differential analysis on... |
| trans_env | Create 'trans_env' object to analyze the association between... |
| trans_func | Create 'trans_func' object for functional prediction. |
| trans_metab | Create 'trans_metab' object for metabolite analysis. |
| trans_mst | Create 'trans_mst' object for microbial source tracking (MST)... |
| trans_multiomics | Multi-omics data integration analysis. |
| trans_network | Create 'trans_network' object for network analysis. |
| trans_niche | Create 'trans_niche' object for niche breadth and niche... |
| trans_norm | Feature abundance normalization/transformation. |
| trans_nullmodel | Create 'trans_nullmodel' object for null model related... |
| trans_phylo | trans_phylo class |
| trans_rarefy | Rarefaction and plotting. |
| trans_venn | Create 'trans_venn' object for the Venn diagram, petal plot... |
