Files in ShawHahnLab/microsat
Computational, High-throughput Individual Identification through Microsatellite Profiling
.Rbuildignore
.circleci/config.yml
.gitignore
DESCRIPTION
GUIDE.Rmd
LICENSE
NAMESPACE
NEWS.md
R/analyze_dataset.R
R/analyze_sample.R
R/analyze_seqs.R
R/categorize.R
R/chiimp.R
R/configuration.R
R/helper_data.R
R/histogram.R
R/installer.R
R/io.R
R/markdown.R
R/primers.R
R/report.R
R/summarize_dataset.R
R/summarize_sample.R
R/util.R
README.md
configure
data/test_data.rda
exec/chiimp
exec/chiimp.cmd
exec/chiimp.command
exec/chiimp.sh
exec/demo.sh
exec/demo_empty.sh
exec/find_pandoc.R
inst/WORDLIST
inst/example_config.csv
inst/example_config.yml
inst/example_locus_attrs.csv
inst/extdata/config_defaults.csv
inst/report/report.Rmd
inst/report/report.css
inst/report/report_alignments.Rmd
inst/report/report_contamination.Rmd
inst/report/report_distances.Rmd
inst/report/report_flag.Rmd
inst/report/report_genotypes.Rmd
inst/report/report_identifications.Rmd
install_linux.sh
install_mac.command
install_windows.cmd
man/CFG_DEFAULTS.Rd
man/CMP.Rd
man/RAW_NT.Rd
man/align_alleles.Rd
man/allele_match.Rd
man/analyze_dataset.Rd
man/analyze_sample.Rd
man/analyze_seqs.Rd
man/apply_config.Rd
man/calc_genotype_distance.Rd
man/categorize_genotype_results.Rd
man/cfg.Rd
man/check_length.Rd
man/check_motif.Rd
man/chiimp-package.Rd
man/find_artifact.Rd
man/find_closest_matches.Rd
man/find_primer_matches.Rd
man/find_stutter.Rd
man/format_pandoc_args.Rd
man/full_analysis.Rd
man/get_px_width.Rd
man/handle_primers.Rd
man/histogram.Rd
man/load_allele_names.Rd
man/load_config.Rd
man/load_config_csv.Rd
man/load_config_yaml.Rd
man/load_csv.Rd
man/load_dataset.Rd
man/load_genotypes.Rd
man/load_locus_attrs.Rd
man/load_seqs.Rd
man/logmsg.Rd
man/main.Rd
man/make_allele_names.Rd
man/make_dist_mat.Rd
man/make_dist_mat_known.Rd
man/make_entry_id.Rd
man/make_raw_nt.Rd
man/make_read_primer_table.Rd
man/make_rownames.Rd
man/match_known_genotypes.Rd
man/name_alleles_in_table.Rd
man/name_known_sequences.Rd
man/order_entries.Rd
man/parse_config.Rd
man/plot_alignment.Rd
man/plot_cts_per_locus.Rd
man/plot_dist_mat.Rd
man/plot_heatmap.Rd
man/plot_heatmap_artifacts.Rd
man/plot_heatmap_homozygous.Rd
man/plot_heatmap_prominent_seqs.Rd
man/plot_heatmap_proportions.Rd
man/plot_heatmap_stutter.Rd
man/prepare_dataset.Rd
man/remove_shared_root_dir.Rd
man/render_report.Rd
man/report_genotypes.Rd
man/report_idents.Rd
man/revcmp.Rd
man/sample_analysis_funcs.Rd
man/sample_summary_funcs.Rd
man/save_alignment_images.Rd
man/save_alignments.Rd
man/save_allele_seqs.Rd
man/save_data.Rd
man/save_dataset.Rd
man/save_dist_mat.Rd
man/save_histograms.Rd
man/save_results_summary.Rd
man/save_sample_data.Rd
man/save_seqfile_data.Rd
man/setup_package.Rd
man/sort_results.Rd
man/str_hist_render.Rd
man/str_hist_setup.Rd
man/str_hist_setup_legend.Rd
man/summarize_attribute.Rd
man/summarize_dataset.Rd
man/summarize_genotypes.Rd
man/summarize_genotypes_known.Rd
man/summarize_sample.Rd
man/tabulate_allele_names.Rd
man/tally_cts_per_locus.Rd
man/test_data.Rd
man/tidy_analyzed_dataset.Rd
man/version_compare.Rd
tests/testthat.R
tests/testthat/data/analyze_dataset/dataset.rds
tests/testthat/data/analyze_dataset/known_alleles.rds
tests/testthat/data/analyze_dataset/locus_attrs.rds
tests/testthat/data/analyze_dataset/results.rds
tests/testthat/data/analyze_dataset/results_known_alleles.rds
tests/testthat/data/analyze_dataset/seqs.rds
tests/testthat/data/analyze_sample/sample_data.rds
tests/testthat/data/analyze_sample/seq_data.rds
tests/testthat/data/analyze_seqs/locus_attrs.rds
tests/testthat/data/analyze_seqs/locus_attrs_rev_primer_mod.rds
tests/testthat/data/analyze_seqs/locus_attrs_rev_primer_revcmp.rds
tests/testthat/data/analyze_seqs/seq_data.rds
tests/testthat/data/analyze_seqs/seq_data_ambig.rds
tests/testthat/data/analyze_seqs/seq_data_artifact.rds
tests/testthat/data/analyze_seqs/seq_data_empty.rds
tests/testthat/data/analyze_seqs/seq_data_rev_primers.rds
tests/testthat/data/analyze_seqs/seq_data_rev_primers_mod.rds
tests/testthat/data/analyze_seqs/seq_data_stubs.rds
tests/testthat/data/analyze_seqs/seq_data_stutter_filter_check.rds
tests/testthat/data/analyze_seqs/seq_data_stutter_threshold_mod.rds
tests/testthat/data/analyze_seqs/seq_data_stutter_threshold_orig.rds
tests/testthat/data/analyze_seqs/seqs.rds
tests/testthat/data/analyze_seqs/seqs_ambig.rds
tests/testthat/data/analyze_seqs/seqs_artifact.rds
tests/testthat/data/analyze_seqs/seqs_stubs.rds
tests/testthat/data/analyze_seqs/seqs_stutter_filter_check.rds
tests/testthat/data/analyze_seqs/seqs_stutter_threshold_check.rds
tests/testthat/data/categorize/categories.rds
tests/testthat/data/categorize/categories_blanks.rds
tests/testthat/data/categorize/categories_drop.rds
tests/testthat/data/categorize/genotypes_known.rds
tests/testthat/data/categorize/match_known_genotypes.rds
tests/testthat/data/categorize/results_summary.rds
tests/testthat/data/categorize/results_summary_matched.rds
tests/testthat/data/categorize/results_summary_matched_blanks.rds
tests/testthat/data/categorize/results_summary_matched_drop.rds
tests/testthat/data/histogram/output.rds
tests/testthat/data/histogram/output_empty_sample_data.rds
tests/testthat/data/histogram/output_seq_data_only.rds
tests/testthat/data/histogram/sample_data.rds
tests/testthat/data/histogram/seq_data.rds
tests/testthat/data/io/config.yml
tests/testthat/data/io/config_unrecognized_key.yml
tests/testthat/data/io/dataset.csv
tests/testthat/data/io/dataset.rds
tests/testthat/data/io/dataset_dups.csv
tests/testthat/data/io/dataset_dups.rds
tests/testthat/data/io/locus_attrs.csv
tests/testthat/data/io/locus_attrs.rds
tests/testthat/data/io/locus_attrs_dups.csv
tests/testthat/data/io/locus_attrs_dups.rds
tests/testthat/data/io/locus_attrs_wrongcol.csv
tests/testthat/data/io/misc.csv
tests/testthat/data/io/misc.csv.rds
tests/testthat/data/io/results.rds
tests/testthat/data/io/seqs.rds
tests/testthat/data/report/alignments.rds
tests/testthat/data/report/allele_summary.rds
tests/testthat/data/report/dist_mat.rds
tests/testthat/data/report/results.rds
tests/testthat/data/report/results_summary.rds
tests/testthat/data/setup_test_data.R
tests/testthat/data/summarize_dataset/alignments.rds
tests/testthat/data/summarize_dataset/alignments_no_derep.rds
tests/testthat/data/summarize_dataset/cts_per_locus.rds
tests/testthat/data/summarize_dataset/dist_mat.rds
tests/testthat/data/summarize_dataset/genotypes_known.rds
tests/testthat/data/summarize_dataset/results.rds
tests/testthat/data/summarize_dataset/results_known.rds
tests/testthat/data/summarize_dataset/results_known_mod.rds
tests/testthat/data/summarize_dataset/results_mod.rds
tests/testthat/data/summarize_sample/sample_data.rds
tests/testthat/data/summarize_sample/sample_data_ambig.rds
tests/testthat/data/summarize_sample/sample_data_empty.rds
tests/testthat/data/summarize_sample/sample_data_guided.rds
tests/testthat/data/summarize_sample/sample_data_guided_empty.rds
tests/testthat/data/summarize_sample/sample_data_guided_flip.rds
tests/testthat/data/summarize_sample/sample_data_guided_no_lens.rds
tests/testthat/data/summarize_sample/sample_data_guided_one_len.rds
tests/testthat/data/summarize_sample/sample_data_low.rds
tests/testthat/data/summarize_sample/sample_data_multi_artifact.rds
tests/testthat/data/summarize_sample/sample_data_multi_stutter.rds
tests/testthat/data/summarize_sample/sample_data_stubs.rds
tests/testthat/data/summarize_sample/sample_data_stutter.rds
tests/testthat/data/summarize_sample/sample_datas_b.rds
tests/testthat/data/summarize_sample/sample_summaries_b.rds
tests/testthat/data/summarize_sample/sample_summary.rds
tests/testthat/data/summarize_sample/sample_summary_ambig.rds
tests/testthat/data/summarize_sample/sample_summary_empty.rds
tests/testthat/data/summarize_sample/sample_summary_guided.rds
tests/testthat/data/summarize_sample/sample_summary_guided_empty.rds
tests/testthat/data/summarize_sample/sample_summary_guided_flip.rds
tests/testthat/data/summarize_sample/sample_summary_guided_no_lens.rds
tests/testthat/data/summarize_sample/sample_summary_guided_one_len.rds
tests/testthat/data/summarize_sample/sample_summary_low.rds
tests/testthat/data/summarize_sample/sample_summary_multi_artifact.rds
tests/testthat/data/summarize_sample/sample_summary_multi_stutter.rds
tests/testthat/data/summarize_sample/sample_summary_stubs.rds
tests/testthat/data/summarize_sample/sample_summary_stutter.rds
tests/testthat/helper.R
tests/testthat/test_analyze_dataset.R
tests/testthat/test_analyze_sample.R
tests/testthat/test_analyze_seqs.R
tests/testthat/test_categorize.R
tests/testthat/test_configuration.R
tests/testthat/test_histogram.R
tests/testthat/test_io.R
tests/testthat/test_primers.R
tests/testthat/test_report.R
tests/testthat/test_summarize_dataset.R
tests/testthat/test_summarize_sample.R
tests/testthat/test_util.R
tools/README.md
tools/check_lint.R
tools/check_spelling.R
tools/chiimp.AppleScript
tools/circleci_install_test.sh
tools/conda_environment.yml
tools/conda_install.sh
tools/install.R
tools/prep_release.sh
tools/render_guide.sh
