Man pages for welch16/microbiome.onglab
Wrapper functions to run dada2 with htCondor
| any_na | function that checks if any element is na in a vector |
| aux_get_matrix | gets the ASV matrix for some samples |
| aux_split_run | splits the ASV matrix according to the negative control... |
| compute_prevalence | computes the prevalence statistics for each ASV |
| condor_error_rates | generate the input to learn the error rates with condor |
| condor_filter_trim | generate the input to filter and trim the fastq files with... |
| condor_generate_all | generates all condor files |
| condor_generate_group_dag | generate the dagman file for running the pipeline with condor |
| condor_label_taxa | generate the input file to label taxa with condor |
| condor_make_sequence_table | generate the input to make the sequence table files with... |
| condor_merge_pairs | generate the input to filter and trim the fastq files with... |
| condor_remove_chimeras | generate the input file to remove chimeras from the sequence... |
| condor_sourcetracker | generates the condor file to performing quality control with... |
| create_file_structure | create the full file structure that integrated across... |
| create_file_structure_group | creates the file structure for running dada2 with condor |
| dada2_param_copy_all | copies all the parameter templates to a directory, and uses a... |
| dada2_param_filter_trim | creates a default param file for the filter and trim process |
| dada2_param_learn_error_rates | creates a default param file for the learn error rates... |
| dada2_param_merge_pairs | creates a default param file for the merge pairs process |
| dada2_param_remove_chimera | creates a default param file for the remove chimera process |
| get_param_chimeras | function to add default parameters to remove_chimeras script |
| get_param_error_rates | function to add default parameters for learn error rates... |
| get_param_filter_trim | function to add default parameters for filter and trim script |
| get_param_merge_pairs | function to add default parameters for merge_pairs script |
| get_param_sourcetracker | function to add default parameters for learn error rates... |
| get_tax_ids | auxiliar function to label the taxa |
| load_sourcetracker | loads sourcetracker code from the raw github repository |
| merge_sourcetracker_results | merge sourcetracker results into a big sourcetracker object |
| parse_filtered_file | converts from input files into the filtered file format for... |
| plot_abundance_per_step | compares the (relative) abundance for each step |
| plot_prevalence | plots the prevalence statistic |
| plot_quality_profiles | plots the quality profiles generated by dada2's... |
| run_diversity_app | Runs a shiny app to perform a diversity analysis |
| save_files | write csv files structured to make the dada2 pipeline run... |
| sourcetracker_parameters | creates a default param file for the source tracker check |
| summarize_number_reads | summarizes the number of reads resulted after each step into... |
| warning_file | creates a warning if the file doesn't exists |
