Files in kevinlkx/Mapgen
Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
Mapgen.Rproj
NAMESPACE
R/annots.R R/development.R R/diagnosis.R R/finemapping.R R/gene_mapping.R R/gwas.R R/harmonization.R R/partition_pips.R R/plots.R R/torus.R R/utils-pipe.R R/utils.R README.Rmd README.md
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/data_preparation_tutorial.html
docs/articles/data_preparation_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/enrichment_tutorial.html
docs/articles/enrichment_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/finemapping_tutorial.html
docs/articles/finemapping_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/finemapping_ukbb_ld_diagnosis.html
docs/articles/finemapping_ukbb_ld_diagnosis_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/diagnosis-plots-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/diagnosis-plots-2.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-2-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-3-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-4-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-5-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-6-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-7-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-8-1.png
docs/articles/finemapping_ukbb_ld_diagnosis_files/figure-html/unnamed-chunk-9-1.png
docs/articles/gene_mapping_tutorial.html
docs/articles/gene_mapping_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/gene_mapping_tutorial_files/figure-html/gene-manhattan-plot-1.png
docs/articles/index.html
docs/articles/make_trackplots.html
docs/articles/make_trackplots_files/figure-html/make-CALU-trackplot-1.png
docs/articles/make_trackplots_files/figure-html/make-HCN4-trackplot-1.png
docs/articles/partition_pip_tutorial.html
docs/articles/partition_pip_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/partition_pip_tutorial_files/figure-html/structure-plot-OCRs-1.png
docs/articles/partition_pip_tutorial_files/figure-html/structure-plot-annots-1.png
docs/articles/track_plot_tutorial.html
docs/articles/track_plot_tutorial_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/track_plot_tutorial_files/figure-html/make-CALU-trackplot-1.png
docs/articles/track_plot_tutorial_files/figure-html/make-HCN4-trackplot-1.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/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/LD_diagnosis_rss.html
docs/reference/LD_diagnosis_susie_rss.html
docs/reference/Rplot001.png
docs/reference/annotate_snps_binary.html
docs/reference/annotator_merged.html
docs/reference/assign_locus_snp.html
docs/reference/assign_snp_locus.html
docs/reference/block_view_summary.html
docs/reference/clean_sumstats.html
docs/reference/compile_structure_plot_data.html
docs/reference/compute_distance_weight.html
docs/reference/compute_gene_pip.html
docs/reference/extract_gene_level_result.html
docs/reference/figures/gene.mapping.diagram.png
docs/reference/figures/workflow.overview.png
docs/reference/find_nearest_genes.html
docs/reference/finemapping_annot_trackplot.html
docs/reference/gene_by_distance.html
docs/reference/gene_cs.html
docs/reference/gene_manhattan_plot.html
docs/reference/gene_view_summary.html
docs/reference/get_UKBB_region_info.html
docs/reference/get_gene_cs.html
docs/reference/get_locus_level_gene_pip.html
docs/reference/get_nearby_interactions.html
docs/reference/harmonize_sumstats_LD.html
docs/reference/index.html
docs/reference/load_UKBB_LDREF.html
docs/reference/make_genomic_annots.html
docs/reference/make_structure_plot.html
docs/reference/match_gwas_LDREF.html
docs/reference/match_gwas_bigsnp.html
docs/reference/merge_bigsnp_gwas.html
docs/reference/merge_susie_sumstats.html
docs/reference/nearby_interactions.html
docs/reference/partition_pip_annots.html
docs/reference/partition_pip_regions.html
docs/reference/pip_structure_plot.html
docs/reference/pipe.html
docs/reference/prepare_susie_data_with_torus_result.html
docs/reference/prepare_torus_input_files.html
docs/reference/process_ABC.html
docs/reference/process_finemapping_sumstats.html
docs/reference/process_gwas_sumstats.html
docs/reference/process_loop_data.html
docs/reference/process_narrowpeaks.html
docs/reference/process_pcHiC.html
docs/reference/read_LD.html
docs/reference/read_LD_SNP_info.html
docs/reference/run_finemapping.html
docs/reference/run_susie.html
docs/reference/run_susie_rss.html
docs/reference/run_torus.html
docs/reference/snp_view_summary.html
docs/reference/structure_plot.html
docs/reference/sum_pip_annots.html
docs/reference/sum_pip_regions.html
docs/reference/susie_finemap_region.html
docs/reference/track_plot.html
docs/sitemap.xml
inst/extdata/AF.finemapping.sumstats.rds
inst/extdata/LD.blocks.EUR.hg19.rds
inst/extdata/OCRs.hg19.gr.rds
inst/extdata/disjoint.OCRs.hg19.grlist.rds
inst/extdata/genomic.annots.hg19.rds
inst/extdata/heart_ventricle-ENCODE_ABC.tsv.gz
inst/extdata/pcHiC.CM.gr.rds
inst/extdata/test.processed.sumstats.rds
inst/extdata/test.sumstats.txt.gz
inst/extdata/test.torus.res.rds
inst/extdata/test_bed_dir/testbed.bed
inst/extdata/test_bed_dir/testbed2.bed
man/LD_diagnosis_susie_rss.Rd man/assign_snp_locus.Rd man/block_view_summary.Rd man/clean_sumstats.Rd man/compute_gene_pip.Rd man/extract_gene_level_result.Rd
man/figures/gene.mapping.diagram.png
man/figures/workflow.overview.png
man/find_nearest_genes.Rd man/gene_cs.Rd man/gene_manhattan_plot.Rd man/gene_view_summary.Rd man/get_UKBB_region_info.Rd man/get_locus_level_gene_pip.Rd man/harmonize_sumstats_LD.Rd man/load_UKBB_LDREF.Rd man/make_genomic_annots.Rd man/match_gwas_LDREF.Rd man/match_gwas_bigsnp.Rd man/merge_susie_sumstats.Rd man/nearby_interactions.Rd man/partition_pip_annots.Rd man/partition_pip_regions.Rd man/pip_structure_plot.Rd man/pipe.Rd man/prepare_susie_data_with_torus_result.Rd man/prepare_torus_input_files.Rd man/process_ABC.Rd man/process_finemapping_sumstats.Rd man/process_gwas_sumstats.Rd man/process_loop_data.Rd man/process_pcHiC.Rd man/read_LD.Rd man/read_LD_SNP_info.Rd man/run_finemapping.Rd man/run_torus.Rd man/snp_view_summary.Rd man/susie_finemap_region.Rd man/track_plot.Rd vignettes/data_preparation_tutorial.Rmd vignettes/enrichment_tutorial.Rmd vignettes/finemapping_tutorial.Rmd vignettes/finemapping_ukbb_ld_diagnosis.Rmd vignettes/gene_mapping_tutorial.Rmd vignettes/partition_pip_tutorial.Rmd vignettes/track_plot_tutorial.Rmd
kevinlkx/Mapgen documentation built on April 2, 2024, 5:48 a.m.