Files in JhuangLab/annovarR
Integrated Framework to Annotate Genetic Variants
.Rbuildignore
.circleci/config.yml
.editorconfig
.gitignore
.vscode/tasks.json
ChangeLog
DESCRIPTION
Dockerfile
LICENSE
Makefile
NAMESPACE
NEWS.md
R/annotation.R
R/annotation.utils.R
R/annotation.utils.initial.R
R/anor.R
R/auto.R
R/build.R
R/convert.R
R/download.R
R/external_function.R
R/external_tools.R
R/get.R
R/utils.R
README.md
_pkgdown.yml
anor.Rproj
docs/404.html
docs/LICENSE-text.html
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docs/articles/database_of_anor.html
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docs/articles/database_of_anor_files/crosstalk-1.1.0.1/js/crosstalk.js
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docs/articles/database_of_anor_files/dt-ext-responsive-1.10.20/js/dataTables.responsive.min.js
docs/articles/database_of_anor_files/htmlwidgets-1.5.1/htmlwidgets.js
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docs/articles/introduction_to_anor.html
docs/articles/introduction_to_anor_files/crosstalk-1.1.0.1/css/crosstalk.css
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docs/articles/introduction_to_anor_files/htmlwidgets-1.5.1/htmlwidgets.js
docs/articles/introduction_to_anor_files/jquery-1.12.4/LICENSE.txt
docs/articles/introduction_to_anor_files/jquery-1.12.4/jquery.min.js
docs/authors.html
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inst/docker/shiny-apache.conf
inst/docker/shiny-server.conf
inst/extdata/config/databases.toml
inst/extdata/demo/DARNED.R
inst/extdata/demo/GDI_full_10282015.txt
inst/extdata/demo/LoFtool_scores.txt
inst/extdata/demo/RADAR2.R
inst/extdata/demo/RVIS_ExAC_4KW.txt
inst/extdata/demo/clinvar.R
inst/extdata/demo/demo.cfg
inst/extdata/demo/example.bed
inst/extdata/demo/example.gff2
inst/extdata/demo/example.gff3
inst/extdata/demo/example.vcf
inst/extdata/demo/hg19_ALL.sites.2015_08.sqlite.sql
inst/extdata/demo/hg19_ALL.sites.2015_08.txt
inst/extdata/demo/hg19_DARNED.sqlite.sql
inst/extdata/demo/hg19_DARNED.txt
inst/extdata/demo/hg19_RADAR2.sqlite.sql
inst/extdata/demo/hg19_RADAR2.txt
inst/extdata/demo/hg19_REDIportal.txt
inst/extdata/demo/hg19_avsnp147.common.txt
inst/extdata/demo/hg19_avsnp147.sqlite.sql
inst/extdata/demo/hg19_avsnp147.txt
inst/extdata/demo/hg19_caddgt10.txt
inst/extdata/demo/hg19_caddgt20.txt
inst/extdata/demo/hg19_clinvar_20170130.sqlite.sql
inst/extdata/demo/hg19_clinvar_20170130.txt
inst/extdata/demo/hg19_cosmic81.sqlite.sql
inst/extdata/demo/hg19_cosmic81.txt
inst/extdata/demo/hg19_cscd_cancer_circrna.txt
inst/extdata/demo/hg19_cscd_common_circrna.txt
inst/extdata/demo/hg19_cscd_normal_circrna.txt
inst/extdata/demo/hg19_dbnsfp30a.txt
inst/extdata/demo/hg19_dbnsfp31a_interpro.txt
inst/extdata/demo/hg19_dbnsfp33a.txt
inst/extdata/demo/hg19_eigen.txt
inst/extdata/demo/hg19_epi_genes_v1.txt
inst/extdata/demo/hg19_exac03.txt
inst/extdata/demo/hg19_exac03nonpsych.txt
inst/extdata/demo/hg19_exac03nontcga.txt
inst/extdata/demo/hg19_gme.txt
inst/extdata/demo/hg19_gnomad_exome.txt
inst/extdata/demo/hg19_gnomad_genome.txt
inst/extdata/demo/hg19_gwava.txt
inst/extdata/demo/hg19_hgnc_coding.txt
inst/extdata/demo/hg19_hrcr1.txt
inst/extdata/demo/hg19_icgc21.txt
inst/extdata/demo/hg19_intervar_20170202.sqlite.sql
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inst/extdata/demo/hg19_kaviar_20150923.txt
inst/extdata/demo/hg19_mcap.txt
inst/extdata/demo/hg19_nci60.txt
inst/extdata/demo/hg19_normal2016sih_wes_ball.txt
inst/extdata/demo/hg19_normal2016sih_wes_nkt.txt
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inst/extdata/demo/hg19_normal2016sih_wgs_dlbcl.txt
inst/extdata/demo/hg19_normal2016sih_wgs_nkt.txt
inst/extdata/demo/hg19_popfreq_all_20150413.txt
inst/extdata/demo/hg19_popfreq_max_20150413.txt
inst/extdata/demo/hg19_refGene.txt
inst/extdata/demo/hg19_revel.txt
inst/extdata/demo/hg19_varcards.txt
inst/extdata/demo/hg38_tmcsnpdb.txt
inst/extdata/demo/interval.R
inst/extdata/demo/snp.test.sqlite.sql
inst/extdata/demo/sqlite.dat.txt
inst/extdata/demo/sqlite/hg19_ALL.sites.2015_08.sqlite
inst/extdata/demo/sqlite/hg19_DARNED.sqlite
inst/extdata/demo/sqlite/hg19_RADAR2.sqlite
inst/extdata/demo/sqlite/hg19_REDIportal.sqlite
inst/extdata/demo/sqlite/hg19_avsnp147.common.sqlite
inst/extdata/demo/sqlite/hg19_avsnp147.sqlite
inst/extdata/demo/sqlite/hg19_caddgt10.sqlite
inst/extdata/demo/sqlite/hg19_caddgt20.sqlite
inst/extdata/demo/sqlite/hg19_clinvar_20170130.sqlite
inst/extdata/demo/sqlite/hg19_cosmic81.sqlite
inst/extdata/demo/sqlite/hg19_dbnsfp30a.sqlite
inst/extdata/demo/sqlite/hg19_dbnsfp31a_interpro.sqlite
inst/extdata/demo/sqlite/hg19_dbnsfp33a.sqlite
inst/extdata/demo/sqlite/hg19_eigen.sqlite
inst/extdata/demo/sqlite/hg19_exac03.sqlite
inst/extdata/demo/sqlite/hg19_exac03nonpsych.sqlite
inst/extdata/demo/sqlite/hg19_exac03nontcga.sqlite
inst/extdata/demo/sqlite/hg19_gme.sqlite
inst/extdata/demo/sqlite/hg19_gnomad_exome.sqlite
inst/extdata/demo/sqlite/hg19_gnomad_genome.sqlite
inst/extdata/demo/sqlite/hg19_gwava.sqlite
inst/extdata/demo/sqlite/hg19_hrcr1.sqlite
inst/extdata/demo/sqlite/hg19_icgc21.sqlite
inst/extdata/demo/sqlite/hg19_intervar_20170202.sqlite
inst/extdata/demo/sqlite/hg19_kaviar_20150923.sqlite
inst/extdata/demo/sqlite/hg19_mcap.sqlite
inst/extdata/demo/sqlite/hg19_nci60.sqlite
inst/extdata/demo/sqlite/hg19_normal2016sih_wes_ball.sqlite
inst/extdata/demo/sqlite/hg19_normal2016sih_wes_nkt.sqlite
inst/extdata/demo/sqlite/hg19_normal2016sih_wes_tall.sqlite
inst/extdata/demo/sqlite/hg19_normal2016sih_wgs_dlbcl.sqlite
inst/extdata/demo/sqlite/hg19_normal2016sih_wgs_nkt.sqlite
inst/extdata/demo/sqlite/hg19_popfreq_all_20150413.sqlite
inst/extdata/demo/sqlite/hg19_popfreq_max_20150413.sqlite
inst/extdata/demo/sqlite/hg19_revel.sqlite
inst/extdata/demo/vcfanno_demo/conf.toml
inst/extdata/demo/vcfanno_demo/custom.lua
inst/extdata/demo/vcfanno_demo/ex.bam
inst/extdata/demo/vcfanno_demo/ex.bam.bai
inst/extdata/demo/vcfanno_demo/exac.vcf.gz
inst/extdata/demo/vcfanno_demo/exac.vcf.gz.tbi
inst/extdata/demo/vcfanno_demo/fitcons.bed.gz
inst/extdata/demo/vcfanno_demo/fitcons.bed.gz.tbi
inst/extdata/demo/vcfanno_demo/gem.conf
inst/extdata/demo/vcfanno_demo/gnomad.conf
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inst/extdata/demo/vcfanno_demo/rare-disease.conf
inst/extdata/demo/vcfanno_demo/rare-disease.lua
inst/extdata/sql/output_file_table.sql
inst/extdata/sql/task_table.sql
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inst/scripts/start.R
man/annotation.Rd
man/annotation.cols.match.Rd
man/annotation.merge.Rd
man/annotation.region.match.Rd
man/annovar.Rd
man/anor.Rd
man/del.Rd
man/download.database.Rd
man/drop.mysql.index.Rd
man/drop.sqlite.index.Rd
man/figures/BRVar_databases-1.jpg
man/figures/annovarR_package-1.jpg
man/figures/logo.png
man/figures/logo.svg
man/figures/opencpu.jpg
man/figures/shiny_app.jpg
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man/get.annotation.dbtype.Rd
man/get.annotation.names.Rd
man/get.annotation.needcols.Rd
man/get.download.name.Rd
man/mysql.auto.build.Rd
man/mysql.auto.index.Rd
man/mysql.build.Rd
man/mysql.head.Rd
man/mysql.index.Rd
man/mysql.tb.colnames.Rd
man/mysql.tb.indexes.Rd
man/sql2sqlite.Rd
man/sqlite.auto.build.Rd
man/sqlite.auto.index.Rd
man/sqlite.build.Rd
man/sqlite.head.Rd
man/sqlite.index.Rd
man/sqlite.tb.colnames.Rd
man/sqlite.tb.indexes.Rd
man/sqlite2sql.Rd
man/vcfanno.Rd
man/vep.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
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pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
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tests/testthat.R
tests/testthat/avoid_32_error/test_region.R
tests/testthat/redundent/test_annotation.R
tests/testthat/test_annotation.reduce.R
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tests/testthat/test_annovar.R
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vignettes/database_of_anor.Rmd
vignettes/introduction_to_anor.Rmd
