Files in jamesdiao/clinvaR

collection, analysis, and visualization tools for ClinVar data

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/annotate.R R/clinvaR.R R/download_1000g.R R/get_clinvar.R R/get_genes.R R/h_read.R R/import_VCF.R R/over_time.R R/var_plot_1000g.R R/zzz.R

README.html

README.md

clinvaR.Rproj

inst/doc/clinvar.R inst/doc/clinvar.Rmd

inst/doc/clinvar.html

inst/doc/clinvar.md

inst/extdata/1000G/refGene.rds

inst/extdata/Archive_Tables/archive_2012.tsv

inst/extdata/Archive_Tables/archive_2013.tsv

inst/extdata/Archive_Tables/archive_2014.tsv

inst/extdata/Archive_Tables/archive_2015.tsv

inst/extdata/Archive_Tables/archive_2016.tsv

inst/extdata/Archive_Tables/archive_2017.tsv

inst/extdata/Archive_Tables/current.tsv

inst/extdata/Init.R inst/extdata/MacArthur_Gene_Lists/README_1.md

inst/extdata/MacArthur_Gene_Lists/lists/BROCA_Cancer_Risk_Panel.tsv

inst/extdata/MacArthur_Gene_Lists/lists/DRG_KangJ.tsv

inst/extdata/MacArthur_Gene_Lists/lists/DRG_WoodRD.tsv

inst/extdata/MacArthur_Gene_Lists/lists/acmg_59.tsv

inst/extdata/MacArthur_Gene_Lists/lists/all_ad.tsv

inst/extdata/MacArthur_Gene_Lists/lists/all_ar.tsv

inst/extdata/MacArthur_Gene_Lists/lists/berg_ad.tsv

inst/extdata/MacArthur_Gene_Lists/lists/berg_ar.tsv

inst/extdata/MacArthur_Gene_Lists/lists/berg_xd.tsv

inst/extdata/MacArthur_Gene_Lists/lists/berg_xr.tsv

inst/extdata/MacArthur_Gene_Lists/lists/blekhman_ad.tsv

inst/extdata/MacArthur_Gene_Lists/lists/blekhman_ar.tsv

inst/extdata/MacArthur_Gene_Lists/lists/blekhman_x.tsv

inst/extdata/MacArthur_Gene_Lists/lists/clingen_level3_genes_2015_02_27.tsv

inst/extdata/MacArthur_Gene_Lists/lists/clinvar_path_likelypath.tsv

inst/extdata/MacArthur_Gene_Lists/lists/core_essentials_hart.tsv

inst/extdata/MacArthur_Gene_Lists/lists/drug_targets_nelson.tsv

inst/extdata/MacArthur_Gene_Lists/lists/fda_approved_drug_targets.tsv

inst/extdata/MacArthur_Gene_Lists/lists/fmrp_list_gencode.tsv

inst/extdata/MacArthur_Gene_Lists/lists/gpcr.tsv

inst/extdata/MacArthur_Gene_Lists/lists/gwascatalog.tsv

inst/extdata/MacArthur_Gene_Lists/lists/kinases.tsv

inst/extdata/MacArthur_Gene_Lists/lists/lmm_hcm.tsv

inst/extdata/MacArthur_Gene_Lists/lists/mgi_essential.tsv

inst/extdata/MacArthur_Gene_Lists/lists/natural_product_targets.tsv

inst/extdata/MacArthur_Gene_Lists/lists/olfactory_receptors.tsv

inst/extdata/MacArthur_Gene_Lists/lists/universe.tsv

inst/extdata/MacArthur_Gene_Lists/lists/x-linked_clinvar.tsv

inst/extdata/MacArthur_Gene_Lists/other_data/drug_gene_match.tsv

inst/extdata/MacArthur_Gene_Lists/other_data/gene_symbol_thesaurus.txt

inst/extdata/MacArthur_Gene_Lists/other_data/omim.full.tsv

inst/extdata/MacArthur_Gene_Lists/other_data/omim.use.tsv

inst/extdata/MacArthur_Gene_Lists/src/BROCA.R inst/extdata/MacArthur_Gene_Lists/src/DRG_WoodRD.R

inst/extdata/MacArthur_Gene_Lists/src/berg_lists.py

inst/extdata/MacArthur_Gene_Lists/src/blekhman_lists.py

inst/extdata/MacArthur_Gene_Lists/src/clinvar_path_likelypath.bash

inst/extdata/MacArthur_Gene_Lists/src/create_universe.bash

inst/extdata/MacArthur_Gene_Lists/src/drug_targets.py

inst/extdata/MacArthur_Gene_Lists/src/gene_list_utils.py

inst/extdata/MacArthur_Gene_Lists/src/gpcr.bash

inst/extdata/MacArthur_Gene_Lists/src/hart_lists.py

inst/extdata/MacArthur_Gene_Lists/src/kinases.bash

inst/extdata/MacArthur_Gene_Lists/src/mgi_essential.py

inst/extdata/MacArthur_Gene_Lists/src/nelson_lists.py

inst/extdata/MacArthur_Gene_Lists/src/olfactory.bash

inst/extdata/MacArthur_Gene_Lists/src/parse_omim.py

inst/extdata/MacArthur_Gene_Lists/src/simplify_omim.py

inst/extdata/MacArthur_Gene_Lists/src/union_lists.py

inst/extdata/MacArthur_Gene_Lists/src/update_symbols.py

inst/extdata/MacArthur_Gene_Lists/src/x-linked_clinvar.R

inst/extdata/RDS/clinvar_2012-06-16.rds

inst/extdata/RDS/clinvar_2012-10-26.rds

inst/extdata/RDS/clinvar_2012-11-05.rds

inst/extdata/RDS/clinvar_2012-12-31.rds

inst/extdata/RDS/clinvar_2013-01-14.rds

inst/extdata/RDS/clinvar_2013-01-18.rds

inst/extdata/RDS/clinvar_2013-02-26.rds

inst/extdata/RDS/clinvar_2013-05-06.rds

inst/extdata/RDS/clinvar_2013-08-08.rds

inst/extdata/RDS/clinvar_2013-09-05.rds

inst/extdata/RDS/clinvar_2013-09-30.rds

inst/extdata/RDS/clinvar_2013-11-05.rds

inst/extdata/RDS/clinvar_2013-12-03.rds

inst/extdata/RDS/clinvar_2013-12-30.rds

inst/extdata/RDS/clinvar_2014-02-11.rds

inst/extdata/RDS/clinvar_2014-03-03.rds

inst/extdata/RDS/clinvar_2014-04-01.rds

inst/extdata/RDS/clinvar_2014-04-30.rds

inst/extdata/RDS/clinvar_2014-06-04.rds

inst/extdata/RDS/clinvar_2014-07-02.rds

inst/extdata/RDS/clinvar_2014-08-07.rds

inst/extdata/RDS/clinvar_2014-09-02.rds

inst/extdata/RDS/clinvar_2014-09-29.rds

inst/extdata/RDS/clinvar_2014-11-05.rds

inst/extdata/RDS/clinvar_2014-12-02.rds

inst/extdata/RDS/clinvar_2015-01-06.rds

inst/extdata/RDS/clinvar_2015-02-03.rds

inst/extdata/RDS/clinvar_2015-03-05.rds

inst/extdata/RDS/clinvar_2015-03-30.rds

inst/extdata/RDS/clinvar_2015-05-04.rds

inst/extdata/RDS/clinvar_2015-06-03.rds

inst/extdata/RDS/clinvar_2015-06-29.rds

inst/extdata/RDS/clinvar_2015-08-04.rds

inst/extdata/RDS/clinvar_2015-09-01.rds

inst/extdata/RDS/clinvar_2015-09-29.rds

inst/extdata/RDS/clinvar_2015-11-02.rds

inst/extdata/RDS/clinvar_2015-12-01.rds

inst/extdata/RDS/clinvar_2016-01-04.rds

inst/extdata/RDS/clinvar_2016-02-03.rds

inst/extdata/RDS/clinvar_2016-03-02.rds

inst/extdata/RDS/clinvar_2016-04-05.rds

inst/extdata/RDS/clinvar_2016-05-02.rds

inst/extdata/RDS/clinvar_2016-05-31.rds

inst/extdata/RDS/clinvar_2016-07-05.rds

inst/extdata/RDS/clinvar_2016-08-02.rds

inst/extdata/RDS/clinvar_2016-08-31.rds

inst/extdata/RDS/clinvar_2016-10-03.rds

inst/extdata/RDS/clinvar_2016-11-01.rds

inst/extdata/RDS/clinvar_2016-11-28.rds

inst/extdata/RDS/clinvar_2017-01-04.rds

inst/extdata/RDS/clinvar_2017-01-30.rds

inst/extdata/RDS/clinvar_2017-02-28.rds

inst/extdata/RDS/clinvar_2017-04-04.rds

inst/extdata/RDS/clinvar_2017-05-01.rds

inst/extdata/RDS/clinvar_2017-05-30.rds

inst/extdata/RDS/clinvar_2017-07-05.rds

inst/extdata/Supplementary_Files/ACMG_SF_v2.0.txt

inst/extdata/Supplementary_Files/clinvar_result_2016_12_04.txt

inst/extdata/Supplementary_Files/mim2gene.txt

inst/extdata/Supplementary_Files/phase3map.txt

inst/extdata/Supplementary_Files/query_input.txt

inst/extdata/Unused_R_Functions/aggregate_calc.R inst/extdata/Unused_R_Functions/aggregate_count.R inst/extdata/Unused_R_Functions/ancestry_penetrance.R inst/extdata/Unused_R_Functions/connect_UCSC.R inst/extdata/Unused_R_Functions/freq_CI.R inst/extdata/Unused_R_Functions/get_ACMG.R inst/extdata/Unused_R_Functions/get_allele_freq.R inst/extdata/Unused_R_Functions/get_penetrance.R inst/extdata/Unused_R_Functions/import_file_exac.R inst/extdata/Unused_R_Functions/merge_clinvar_exac_gnomad.R inst/extdata/Unused_R_Functions/prettyprint.R inst/extdata/Unused_R_Functions/var_plot_exac_gnomad.R man/annotate_1000g.Rd man/clinvaR-package.Rd man/delete_downloads.Rd man/download_1000g.Rd man/download_clinvar.Rd man/get_clinvar.Rd man/get_closest_date.Rd man/get_date_list.Rd man/get_genes.Rd man/h_read.Rd man/import_file_1000g.Rd man/over_time.Rd man/plot.annotated_vcf.Rd man/plot.freq_dates.Rd man/plot.penetrance_dates.Rd man/plot.plain_vcf.Rd man/plot.significance_dates.Rd man/plot.submission_dates.Rd man/prettyprint.Rd man/update_clinvar.Rd man/var_plot_1000g.Rd vignettes/clinvar.Rmd

vignettes/clinvar_cache/html/__packages

vignettes/clinvar_cache/html/unnamed-chunk-10_206b8e89d6cceaf100e831268a92ca34.RData

vignettes/clinvar_cache/html/unnamed-chunk-10_206b8e89d6cceaf100e831268a92ca34.rdb

vignettes/clinvar_cache/html/unnamed-chunk-10_206b8e89d6cceaf100e831268a92ca34.rdx

vignettes/clinvar_cache/html/unnamed-chunk-11_ace308a51c49377787b403d7e3790510.RData

vignettes/clinvar_cache/html/unnamed-chunk-11_ace308a51c49377787b403d7e3790510.rdb

vignettes/clinvar_cache/html/unnamed-chunk-11_ace308a51c49377787b403d7e3790510.rdx

vignettes/clinvar_cache/html/unnamed-chunk-12_e3ebc3e60f69c284e094624c871943ff.RData

vignettes/clinvar_cache/html/unnamed-chunk-12_e3ebc3e60f69c284e094624c871943ff.rdb

vignettes/clinvar_cache/html/unnamed-chunk-12_e3ebc3e60f69c284e094624c871943ff.rdx

vignettes/clinvar_cache/html/unnamed-chunk-13_66860e744c2b58f2108796c2865ff7ee.RData

vignettes/clinvar_cache/html/unnamed-chunk-13_66860e744c2b58f2108796c2865ff7ee.rdb

vignettes/clinvar_cache/html/unnamed-chunk-13_66860e744c2b58f2108796c2865ff7ee.rdx

vignettes/clinvar_cache/html/unnamed-chunk-1_ffdaae39c0c14987254e2585c333058f.RData

vignettes/clinvar_cache/html/unnamed-chunk-1_ffdaae39c0c14987254e2585c333058f.rdb

vignettes/clinvar_cache/html/unnamed-chunk-1_ffdaae39c0c14987254e2585c333058f.rdx

vignettes/clinvar_cache/html/unnamed-chunk-2_2871190e468ad77c7d4f8475c4d7c942.RData

vignettes/clinvar_cache/html/unnamed-chunk-2_2871190e468ad77c7d4f8475c4d7c942.rdb

vignettes/clinvar_cache/html/unnamed-chunk-2_2871190e468ad77c7d4f8475c4d7c942.rdx

vignettes/clinvar_cache/html/unnamed-chunk-3_3d9a76fc18bd3b56741531b631347253.RData

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vignettes/clinvar_cache/html/unnamed-chunk-7_d03a3b1d46dada0bdce788485f8ab7b3.RData

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vignettes/clinvar_cache/html/unnamed-chunk-7_d03a3b1d46dada0bdce788485f8ab7b3.rdx

vignettes/clinvar_cache/html/unnamed-chunk-8_5945b44013f2f1623a48924be898fe08.RData

vignettes/clinvar_cache/html/unnamed-chunk-8_5945b44013f2f1623a48924be898fe08.rdb

vignettes/clinvar_cache/html/unnamed-chunk-8_5945b44013f2f1623a48924be898fe08.rdx

vignettes/clinvar_cache/html/unnamed-chunk-9_bf83913994adfc9482a908e4454c19ab.RData

vignettes/clinvar_cache/html/unnamed-chunk-9_bf83913994adfc9482a908e4454c19ab.rdb

vignettes/clinvar_cache/html/unnamed-chunk-9_bf83913994adfc9482a908e4454c19ab.rdx

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jamesdiao/clinvaR documentation built on May 18, 2019, 11:19 a.m.