Files in surh/HMVAR

Human Microbiome Variant Analysis in R

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/Fst.r R/annots.r R/calculate_prevalence.r R/dos.r R/exports.r R/genome_wide_ni.r R/input.r R/metawas.r R/midas_data.r R/mktest.r R/on_attach.r R/other.r R/phylotype2rdp.r R/plotgg_manhattan.r R/plotgg_stacked_columns.r R/pval_qqplot.r R/qp_genotypes.r R/read_eggnog.r R/sequence.r R/singletons.r R/utils.r R/varsites.r README.md

docs/LICENSE-text.html

docs/authors.html

docs/docsearch.css

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

inst/bin/annotation_enrichments.r inst/bin/benchmark_imputation.r

inst/bin/calculate_fst.nf

inst/bin/calculate_fst.r inst/bin/calculate_neutrality_index.r inst/bin/check_mk_pvals.r inst/bin/dos.r inst/bin/genome_metawas.r inst/bin/mktest.r inst/bin/processing/cor.r inst/bin/processing/get_selected_mktest.r inst/bin/processing/plot_genes.r inst/bin/rer_functional_enrichment.r inst/bin/subset_snps.r inst/bin/varsites.r inst/scripts/abundances_by_group.r inst/scripts/analyze_all_pvals.r inst/scripts/analyze_ratio.r inst/scripts/analyze_snps.r inst/scripts/bugwas.r inst/scripts/check_pvals.r inst/scripts/dos_enrichments.r inst/scripts/flipping_impute_test.r inst/scripts/functions.r

inst/scripts/genomewide_ni.txt

inst/scripts/get_all_mktest_genes.r inst/scripts/get_gene_alns.r inst/scripts/hmp16s_1.hmmcp_prevalence.r inst/scripts/hmp16s_2.hmqcp_prevalence.r inst/scripts/hmp16s_3.combine_prevalence.r inst/scripts/imputation_test_mice.r inst/scripts/impute_check_nonposdef.r inst/scripts/lmm_vs_mktest.r inst/scripts/manhattan_type.r inst/scripts/match_snps_genes.r inst/scripts/metawas_overall_enrich.r inst/scripts/mktest_enrichments.r inst/scripts/mktest_vs_metawas.r inst/scripts/plot_fsts.r inst/scripts/plot_mkres_results.r inst/scripts/plot_ni_phylo.r inst/scripts/plot_vwma_pvals.r inst/scripts/plots_for_labmtg.r inst/scripts/poolfstat.r inst/scripts/process_go_enrich_pvals.r

inst/scripts/prop_significant.nf

inst/scripts/prop_significant.r inst/scripts/test_signal_peptide.r inst/scripts/topgo_examples.r inst/scripts/toy_example_examples.r inst/toy_example/README.md

inst/toy_example/map.txt

inst/toy_example/merged.snps/snps_depth.txt

inst/toy_example/merged.snps/snps_freq.txt

inst/toy_example/merged.snps/snps_info.txt

man/annotate_gos.Rd man/annots_to_geneGO.Rd man/assign_allele.Rd man/benchmark_imputation.Rd man/bimbam_impute.Rd man/calculate_dos.Rd man/calculate_fst.Rd man/calculate_mktable.Rd man/calculate_p_error.Rd man/calculate_prevalence.Rd man/check_map.Rd man/check_midas_data.Rd man/check_pvals_in_file.Rd man/check_pvalues.Rd man/determine_sample_dist.Rd man/determine_snp_dist.Rd man/determine_snp_effect.Rd man/determine_substitution_type.Rd man/dos.Rd man/expand_annot.Rd man/find_singletons.Rd man/format_input.Rd man/format_input_hmqcp.Rd man/gemma_kinship.Rd man/gemma_lmm.Rd man/gene_midas_data.Rd man/gene_sel_fun.Rd man/gene_snv_aln.Rd man/genome_wide_ni.Rd man/get_mk_results_files.Rd man/get_sequence_fragment.Rd man/get_site_dist.Rd man/group_size.Rd man/gsea.Rd man/match_freq_and_depth.Rd man/mice_impute.Rd man/midas_dos.Rd man/midas_mktest.Rd man/midas_to_bimbam.Rd man/mktest.Rd man/mkvalues.Rd man/phylotype2rdp.Rd man/phylotype2rdp2.Rd man/plotgg_manhattan.Rd man/plotgg_stacked_columns.Rd man/pval_qqplot.Rd man/qp_genotypes.Rd man/read_eggnog.Rd man/read_midas_abun.Rd man/read_midas_data.Rd man/read_midas_info.Rd man/reexports.Rd man/run_command.Rd man/select_samples_from_abun.Rd man/sign_test.Rd man/site_fst.Rd man/term_gsea.Rd man/terms_enrichment.Rd man/test_go.Rd man/test_singleton_enrichment.Rd man/tidy_mice.Rd man/variable_dist_per_site.Rd man/varsites_pipeline.Rd man/window_fst.Rd tests/testthat.R tests/testthat/test.annots.r tests/testthat/test.dos.r tests/testthat/test.manhattan.r tests/testthat/test.mktest.r tests/testthat/test.utils.r tests/testthat/test.varsites.r

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.