API for AlmaasLab/micInt
Find microbial interactions
| Global functions | |
|---|---|
| Bin | Source code |
| DecodeInputCAArguments | Source code |
| OTU_stats | Man page Source code |
| OTU_time_series | Man page |
| OTU_time_series,data.frame,numeric-method | Man page |
| OTU_time_series,otu_table,numeric-method | Man page |
| OTU_time_series,phyloseq,character-method | Man page |
| OTU_time_series,phyloseq,numeric-method | Man page |
| OTU_time_series-class | Man page |
| abundanceProduct | Source code |
| add_outputargs | Source code |
| as.edgelist | Man page Source code |
| as.edgelist.interaction_table | Man page Source code |
| autoplot.cvLV | Man page Source code |
| autoplot.interaction_table | Man page Source code |
| bootstrap.method.calcn | Source code |
| bootstrap.procedure.memory.optimized | Source code |
| bootstrap.procedure.simple | Source code |
| calculate.z.stat.and.p.value | Source code |
| calculate_q_values | Source code |
| calculate_q_values_vector | Source code |
| ccrepe | Man page Source code |
| ccrepe-package | Man page |
| ccrepeSampleTestFunction | Man page |
| ccrepe_analysis | Man page Source code |
| ccrepe_norm | Source code |
| ccrepe_process_one_dataset | Source code |
| ccrepe_process_two_datasets | Source code |
| check_data_values | Source code |
| clean_common_area_after_processing | Source code |
| collapse_taxonomy | Man page Source code |
| countInteractions | Man page Source code |
| count_matches | Source code |
| create_ccrepe_jobs | Source code |
| create_interaction_table | Man page Source code |
| create_prefix | Man page Source code |
| cut_abundances | Source code |
| cv.LV | Man page Source code |
| edgelist | Man page |
| extractCor | Source code |
| extract_OTUs | Source code |
| extract_integral_system | Source code |
| extract_log_integral_system | Source code |
| filter_dataset | Source code |
| integralSystem | Man page Source code |
| lappend | Source code |
| log.processing.progress | Source code |
| mean_scale | Man page Source code |
| merge_two_matrices | Source code |
| micInt | Man page |
| micInt-package | Man page |
| nc.score | Man page |
| noisificationTemplate | Source code |
| noisify | Man page Source code |
| output_ccrepe_data | Man page Source code |
| permute | Source code |
| plot_trajectory | Man page Source code |
| predict.LV | Man page Source code |
| preprocess_data | Source code |
| preprocess_nc_score_input | Source code |
| print.dist | Source code |
| process_min_abundance_min_samples | Source code |
| process_wrapper_input | Source code |
| qc_filter | Source code |
| ratio_shared_interactions | Man page Source code |
| refine_data | Man page Source code |
| remove_metadata | Source code |
| renormalize | Source code |
| resample | Source code |
| ridge_fit | Man page Source code |
| runAnalysis | Man page Source code |
| scalationTemplate | Source code |
| scale_by_column | Man page Source code |
| seawater | Man page |
| sim.measure | Man page Source code |
| sim.measure-class | Man page |
| sim.measure.attributes | Man page |
| sim.measure.attributes,character-method | Man page |
| sim.measure.attributes,sim.measure-method | Man page |
| sim.measure.attributes-class | Man page |
| sim_measure_function | Man page |
| sim_measure_function,sim.measure-method | Man page |
| similarity_measures | Man page Source code |
| stack_equations | Man page Source code |
| subdivide_by_environment | Man page Source code |
| summary.interaction_table | Man page Source code |
| system_equation | Source code |
| test_LV_fit | Source code |
| try.reboot.again | Source code |
| write.interaction_table | Man page Source code |
