Files in hemstrow/snpR
Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE.md
LICENSE.note
NAMESPACE
NEWS.md
R/NeEstimator_interface.R
R/association_functions.R
R/bootstrapping_functions.R
R/colony_interface.R
R/dataset_documentation.R
R/easypop_interface.R
R/import_functions.R
R/import_wrappers.R
R/internals.R
R/plotting_functions.R
R/pophelper_redistribution.R
R/sequoia_interface.R
R/sfs_functions.R
R/smoothing_functions.R
R/snpRdata.R
R/snpRdata_methods.R
R/stat_functions.R
R/sysdata.rda
R/utility_functions.R
R/zzz.R
README.Rmd
README.md
R_dev/2d_sfs_example_data_projection.RDS
R_dev/abba_baba_attempts.R
R_dev/abba_baba_test_data.RDS
R_dev/abba_baba_work.R
R_dev/afs2d.R
R_dev/depreciated_functions.R
R_dev/function_development.R
R_dev/make_abba_baba_test_data.R
R_dev/plot_pedigree_dev.R
R_dev/stick_faststructure_1k.str
codecov.yml
cran-comments.md
data-raw/internal_data.R
data-raw/steelMSATs.R
data-raw/steelRAW.R
data-raw/stickPED.R
data-raw/stickRAW.R
data-raw/stickSNPs.R
data/steelMSATs.rda
data/steelRAW.rda
data/stickPED.rda
data/stickRAW.rda
data/stickSNPs.rda
inst/CITATION
inst/extdata/snpR_citations.bib
inst/extdata/steelhead_msats.txt
inst/extdata/stick_NN_input.txt
inst/extdata/test_ped.csv
inst/shiny/ui_app/app.R
inst/shiny/ui_app/app_code.R
man/Facets_in_snpR.Rd
man/calc_abba_baba.Rd
man/calc_association.Rd
man/calc_basic_snp_stats.Rd
man/calc_directionality.Rd
man/calc_fis.Rd
man/calc_fst.Rd
man/calc_genetic_distances.Rd
man/calc_isolation_by_distance.Rd
man/calc_ne.Rd
man/calc_p_from_bootstraps.Rd
man/calc_pairwise_ld.Rd
man/calc_prop_poly.Rd
man/calc_seg_sites.Rd
man/calc_sfs.Rd
man/calc_single_stats.Rd
man/calc_smoothed_averages.Rd
man/calc_tajimas_d.Rd
man/calc_tree.Rd
man/check_duplicates.Rd
man/citations.Rd
man/colony_interface.Rd
man/cross_validate_genomic_prediction.Rd
man/do_bootstraps.Rd
man/extract_snpRdata.Rd
man/filter_snps.Rd
man/filters.Rd
man/format_snps.Rd
man/gap_snps.Rd
man/gaussian_weight.Rd
man/get.snpR.stats.Rd
man/import.snpR.data.Rd
man/individual_heterozygosity.Rd
man/is.snpRdata.Rd
man/make_SFS.Rd
man/merge_snpRdata.Rd
man/plot_clusters.Rd
man/plot_diagnostic.Rd
man/plot_manhattan.Rd
man/plot_pairwise_fst_heatmap.Rd
man/plot_pairwise_ld_heatmap.Rd
man/plot_qq.Rd
man/plot_sfs.Rd
man/plot_structure.Rd
man/plot_structure_map.Rd
man/run_genomic_prediction.Rd
man/run_random_forest.Rd
man/run_sequoia.Rd
man/show-snpRdata-method.Rd
man/snpR_import_wrappers.Rd
man/snpRdata-class.Rd
man/snpRdata_dims.Rd
man/steelMSATs.Rd
man/steelRAW.Rd
man/stickPED.Rd
man/stickRAW.Rd
man/stickSNPs.Rd
man/subset_snpRdata.Rd
man/summarize_facets.Rd
man/tabulate_allele_frequency_matrix.Rd
tests/testthat.R
tests/testthat/_snaps/fst_ld.md
tests/testthat/_snaps/interfaces.md
tests/testthat/test-abba_baba.R
tests/testthat/test-association.R
tests/testthat/test-basic_stats.R
tests/testthat/test-filter.R
tests/testthat/test-format.R
tests/testthat/test-fst_ld.R
tests/testthat/test-fwe.R
tests/testthat/test-ibd_dist.R
tests/testthat/test-import.R
tests/testthat/test-interfaces.R
tests/testthat/test-merging.R
tests/testthat/test-misc_get_snpR_stats.R
tests/testthat/test-plotting.R
tests/testthat/test-sfs.R
tests/testthat/test-smoothing.R
tests/testthat/test-snpR_object_creation.R
tests/testthat/test-subset.R
tests/testthat/test_bootstraps.R
vignettes/exportstable.csv
vignettes/snpR_introduction.Rmd
