Man pages for thierrygosselin/stackr
Run stacks pipeline for RADseq analysis inside R
| build_stackr_workflow_dir | Automatically build the stacks/stackr workflow directories |
| change_pop_names | Transform into a factor the POP_ID column, change names and... |
| clean_fq_filename | clean_fq_filename |
| clean_ind_names | clean individual's name |
| clean_markers_names | Clean marker's name |
| clean_pop_names | Clean population's name |
| compound_assignment_pipe_operator | compound assignment pipe operator |
| Exposition_pipe_operator | Exposition pipe-operator |
| extract_catalog_sql_ids | Extract sample SQL IDs from STACKS catalog file |
| fq_file_type | fq_file_type |
| list_sample_file | list_sample_file |
| loc_pop_stats | loc_pop_stats |
| merge_bam | merge_bam |
| merge_fq | merge_fq |
| merge_parallel | merge_parallel |
| mismatch_dir | Generate mismatch directory |
| mismatch_fig | mismatch_fig |
| n | The number of observations in the current group. |
| pi | pi |
| pipe | Forward-pipe operator |
| pi_pop | pi_pop |
| read_stacks_ustacks_log | Read stacks ustacks log |
| rename_fq | Rename fastq files |
| run_cstacks | Run STACKS cstacks module |
| run_gstacks | Run STACKS new module called gstacks |
| run_populations | Run STACKS Version >= 2.0 populations module |
| run_process_radtags | Run STACKS process_radtags module |
| run_radproc | Run RADproc |
| run_split_cstacks | run_split_cstacks |
| run_sstacks | Run STACKS sstacks module |
| run_tsv2bam | Run STACKS tsv2bam and merges BAM files |
| run_ustacks | Run STACKS ustacks module |
| run_ustacks_one_sample | run_ustacks_one_sample |
| separate_haplo | separate_haplo |
| separate_haplo_long | separate_haplo_long |
| split_bam_list | split_bam_list |
| split_pop_map | split_pop_map |
| split_tibble_rows | split_tibble_rows |
| split_vec_row | split_vec_row |
| stackr_future | radiator parallel function |
| stackr_parallel | hack to switch function for parallel computation based on OS |
| stats_stackr | stats_stackr |
| strata_haplo | strata_haplo |
| summary_catalog_log_lik | Summary of catalog log likelihood |
| summary_cstacks | Summarize STACKS cstacks log file generated by stackr |
| summary_genotypes | Summary of 'batch_x.genotypes.txt' and 'batch_x.markers.tsv'... |
| summary_haplotypes | Haplotypes file summary |
| summary_pstacks | Summarize STACKS pstacks files |
| summary_sstacks | Summarize STACKS sstacks log file generated by stackr |
| summary_ustacks | Summarize STACKS ustacks files |
