Files in thierrygosselin/stackr

Run stacks software pipeline for RADseq analysis inside R

.DS_Store

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

NAMESPACE

NEWS.md R/build_stackr_workflow_dir.R R/clean_fq.R R/extract_catalog_sample.R R/global_variables.R R/normalize_reads.R R/read_counter.R R/read_depth_plot.R R/reads_length_distribution.R R/rename_fq.R R/run_cstacks.R R/run_gstacks.R R/run_populations.R R/run_process_radtags.R R/run_radproc.R R/run_sstacks.R R/run_tsv2bam.R R/run_ustacks.R R/stackr_parallel.R R/summary_catalog_log_lik.R R/summary_cstacks.R R/summary_genotypes.R R/summary_haplotypes.R R/summary_pstacks.R R/summary_reads.R R/summary_sstacks.R R/summary_ustacks.R R/utils.R README.Rmd README.md

_pkgdown.yml

appveyor.yml

docs/404.html

docs/articles/index.html

docs/articles/ion_torrent_1.png

docs/articles/ion_torrent_2.png

docs/articles/mismatches.plot.png

docs/articles/mismatches.summary.1.png

docs/articles/mismatches.summary.2.png

docs/articles/read_depth_coverage_groups.png

docs/articles/read_distribution.png

docs/articles/rstudio.project.1.png

docs/articles/rstudio.project.2.png

docs/articles/stackr.html

docs/articles/stackr_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/stackr_files/anchor-sections-1.0/anchor-sections.css

docs/articles/stackr_files/anchor-sections-1.0/anchor-sections.js

docs/articles/stackr_workflow.png

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Exposition_pipe_operator.html

docs/reference/Rplot001.png

docs/reference/build_stackr_workflow_dir.html

docs/reference/change_pop_names.html

docs/reference/check_fq.html

docs/reference/clean_fq.html

docs/reference/clean_fq_filename.html

docs/reference/clean_ind_names.html

docs/reference/clean_markers_names.html

docs/reference/clean_pop_names.html

docs/reference/compound_assignment_pipe_operator.html

docs/reference/extract_catalog_sql_ids.html

docs/reference/fq_file_type.html

docs/reference/index.html

docs/reference/list_sample_file.html

docs/reference/loc_pop_stats.html

docs/reference/merge_bam.html

docs/reference/merge_fq.html

docs/reference/merge_parallel.html

docs/reference/mismatch_dir.html

docs/reference/mismatch_fig.html

docs/reference/n.html

docs/reference/normalize_reads.html

docs/reference/pi.html

docs/reference/pi_pop.html

docs/reference/pipe.html

docs/reference/read_count_one.html

docs/reference/read_counter.html

docs/reference/read_depth_plot.html

docs/reference/read_stacks_ustacks_log.html

docs/reference/reads_length_distribution.html

docs/reference/reads_stats.html

docs/reference/rename_fq.html

docs/reference/run_cstacks.html

docs/reference/run_gstacks.html

docs/reference/run_populations.html

docs/reference/run_process_radtags.html

docs/reference/run_radproc.html

docs/reference/run_split_cstacks.html

docs/reference/run_sstacks.html

docs/reference/run_tsv2bam.html

docs/reference/run_ustacks.html

docs/reference/run_ustacks_one_sample.html

docs/reference/separate_haplo.html

docs/reference/separate_haplo_long.html

docs/reference/split_bam_list.html

docs/reference/split_pop_map.html

docs/reference/split_tibble_rows.html

docs/reference/split_vec_row.html

docs/reference/stackr_normalize.html

docs/reference/stackr_parallel.html

docs/reference/stats_stackr.html

docs/reference/strata_haplo.html

docs/reference/summary_catalog_log_lik.html

docs/reference/summary_cstacks.html

docs/reference/summary_genotypes.html

docs/reference/summary_haplotypes.html

docs/reference/summary_pstacks.html

docs/reference/summary_reads.html

docs/reference/summary_sstacks.html

docs/reference/summary_ustacks.html

docs/reference/write_normalize.html

inst/CITATION

man/.Rapp.history

man/Exposition_pipe_operator.Rd man/build_stackr_workflow_dir.Rd man/change_pop_names.Rd man/check_fq.Rd man/clean_fq.Rd man/clean_fq_filename.Rd man/clean_ind_names.Rd man/clean_markers_names.Rd man/clean_pop_names.Rd man/compound_assignment_pipe_operator.Rd man/extract_catalog_sql_ids.Rd man/fq_file_type.Rd man/list_sample_file.Rd man/loc_pop_stats.Rd man/merge_bam.Rd man/merge_fq.Rd man/merge_parallel.Rd man/mismatch_dir.Rd man/mismatch_fig.Rd man/n.Rd man/normalize_reads.Rd man/pi.Rd man/pi_pop.Rd man/pipe.Rd man/read_count_one.Rd man/read_counter.Rd man/read_depth_plot.Rd man/read_stacks_ustacks_log.Rd man/reads_length_distribution.Rd man/reads_stats.Rd man/rename_fq.Rd man/run_cstacks.Rd man/run_gstacks.Rd man/run_populations.Rd man/run_process_radtags.Rd man/run_radproc.Rd man/run_split_cstacks.Rd man/run_sstacks.Rd man/run_tsv2bam.Rd man/run_ustacks.Rd man/run_ustacks_one_sample.Rd man/separate_haplo.Rd man/separate_haplo_long.Rd man/split_bam_list.Rd man/split_pop_map.Rd man/split_tibble_rows.Rd man/split_vec_row.Rd man/stackr_normalize.Rd man/stackr_parallel.Rd man/stats_stackr.Rd man/strata_haplo.Rd man/summary_catalog_log_lik.Rd man/summary_cstacks.Rd man/summary_genotypes.Rd man/summary_haplotypes.Rd man/summary_pstacks.Rd man/summary_reads.Rd man/summary_sstacks.Rd man/summary_ustacks.Rd man/write_normalize.Rd

stackr.Rproj

vignettes/RADseq_workflow.png

vignettes/ion_torrent_1.png

vignettes/ion_torrent_2.png

vignettes/mismatches.plot.png

vignettes/mismatches.summary.1.png

vignettes/mismatches.summary.2.png

vignettes/read_depth_coverage_groups.png

vignettes/read_distribution.png

vignettes/rstudio.project.1.png

vignettes/rstudio.project.2.png

vignettes/stackr.html

vignettes/stackr_workflow.png

thierrygosselin/stackr documentation built on Nov. 11, 2020, 11 a.m.