├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── AllClasses.R ├── AllGenerics.R ├── AllUtilities.R ├── makeVRangesFromGRanges.R ├── methods-CollapsedVCF-class.R ├── methods-ExpandedVCF-class.R ├── methods-PROVEANDb.class.R ├── methods-PolyPhenDb-class.R ├── methods-SIFTDb-class.R ├── methods-ScanVcfParam-class.R ├── methods-VCF-class.R ├── methods-VCFHeader-class.R ├── methods-VRanges-class.R ├── methods-VRangesList-class.R ├── methods-VariantType-class.R ├── methods-VcfFile.R ├── methods-expand.R ├── methods-filterVcf.R ├── methods-genotypeToSnpMatrix.R ├── methods-import.R ├── methods-locateVariants.R ├── methods-predictCoding.R ├── methods-readVcf.R ├── methods-scanVcf.R ├── methods-scanVcfHeader.R ├── methods-snpSummary.R ├── methods-summarizeVariants.R ├── methods-writeVcf.R ├── test_VariantAnnotation_package.R └── use_vep_api.R ├── inst ├── CITATION ├── extdata │ ├── chr22.vcf.gz │ ├── chr22.vcf.gz.tbi │ ├── chr7-sub.vcf.gz │ ├── chr7-sub.vcf.gz.tbi │ ├── ex2.vcf │ ├── gl_chr1.vcf │ ├── h1187-10k.vcf.gz │ ├── h1187-10k.vcf.gz.tbi │ ├── hapmap_exome_chr22.vcf.gz │ ├── hapmap_exome_chr22.vcf.gz.tbi │ └── structural.vcf ├── scripts │ └── test_Rplinkseq.R └── unitTests │ ├── cases │ ├── FORMAT_header_no_SAMPLEs.vcf │ ├── VarScan_header.vcf │ ├── banded_gvcf.vcf │ ├── buffer_realloc.vcf │ ├── ex1-seq1-90.vcf │ ├── expand.vcf │ ├── fewer-FORMAT-than-GENO.vcf │ ├── meta_header.vcf │ ├── missing-FORMAT-metadata-elt.vcf │ ├── mixedStructural.vcf │ ├── multiple_INFO_fields.vcf │ ├── negative_FORMAT_Number.vcf │ ├── no_FORMAT_column.vcf │ ├── no_GENO_row.vcf │ ├── no_INFO_header.vcf │ └── unspecified_INFO_FORMAT_fields.vcf │ ├── test_SIFTandPolyPhen.R │ ├── test_ScanVcfParam-class.R │ ├── test_VCF-class.R │ ├── test_VRanges-class.R │ ├── test_expand-methods.R │ ├── test_filterVcf.R │ ├── test_genotypeToSnpMatrix.R │ ├── test_isSNV.R │ ├── test_locateVariants-methods.R │ ├── test_predictCoding-methods.R │ ├── test_readVcf-methods.R │ ├── test_scanVcf.R │ ├── test_snpSummary.R │ ├── test_summarizeVariants-methods.R │ ├── test_vcfFields.R │ └── test_writeVcf-methods.R ├── man ├── GLtoGP.Rd ├── PROVEANDb-class.Rd ├── PolyPhenDb-class.Rd ├── PolyPhenDbColumns.Rd ├── SIFTDb-class.Rd ├── SIFTDbColumns.Rd ├── ScanVcfParam-class.Rd ├── VCF-class.Rd ├── VCFHeader-class.Rd ├── VRanges-class.Rd ├── VRangesList-class.Rd ├── VariantType-class.Rd ├── VcfFile-class.Rd ├── defunct.Rd ├── filterVcf-methods.Rd ├── genotypeToSnpMatrix-methods.Rd ├── getTranscriptSeqs-methods.Rd ├── indexVcf-method.Rd ├── isSNV-methods.Rd ├── locateVariants-methods.Rd ├── post_Hs_region.Rd ├── predictCoding-methods.Rd ├── probabilityToSnpMatrix.Rd ├── readVcf-methods.Rd ├── scanVcf-methods.Rd ├── seqinfo-method.Rd ├── snpSummary.Rd ├── summarizeVariants-methods.Rd ├── variant_body.Rd ├── vep_by_region.Rd └── writeVcf-methods.Rd ├── src ├── Biostrings_stubs.c ├── IRanges_stubs.c ├── Makevars ├── R_init_VariantAnnotation.c ├── XVector_stubs.c ├── dna_hash.c ├── dna_hash.h ├── rle.c ├── rle.h ├── strhash.c ├── strhash.h ├── utilities.c ├── utilities.h ├── vcffile.c ├── vcffile.h ├── vcftype.c ├── vcftype.h ├── writevcf.c └── writevcf.h ├── tests └── VariantAnnotation_unit_tests.R └── vignettes ├── VariantAnnotation.Rmd ├── bioinformatics.csl ├── ens.bib ├── ensemblVEP.Rmd ├── filterVcf.Rmd └── filterVcf.bib /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/NEWS -------------------------------------------------------------------------------- /R/AllClasses.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/AllClasses.R -------------------------------------------------------------------------------- /R/AllGenerics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/AllGenerics.R -------------------------------------------------------------------------------- /R/AllUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/AllUtilities.R -------------------------------------------------------------------------------- /R/makeVRangesFromGRanges.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/makeVRangesFromGRanges.R -------------------------------------------------------------------------------- /R/methods-CollapsedVCF-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-CollapsedVCF-class.R -------------------------------------------------------------------------------- /R/methods-ExpandedVCF-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-ExpandedVCF-class.R -------------------------------------------------------------------------------- /R/methods-PROVEANDb.class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-PROVEANDb.class.R -------------------------------------------------------------------------------- /R/methods-PolyPhenDb-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-PolyPhenDb-class.R -------------------------------------------------------------------------------- /R/methods-SIFTDb-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-SIFTDb-class.R -------------------------------------------------------------------------------- /R/methods-ScanVcfParam-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-ScanVcfParam-class.R -------------------------------------------------------------------------------- /R/methods-VCF-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-VCF-class.R -------------------------------------------------------------------------------- /R/methods-VCFHeader-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-VCFHeader-class.R -------------------------------------------------------------------------------- /R/methods-VRanges-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-VRanges-class.R -------------------------------------------------------------------------------- /R/methods-VRangesList-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-VRangesList-class.R -------------------------------------------------------------------------------- /R/methods-VariantType-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-VariantType-class.R -------------------------------------------------------------------------------- /R/methods-VcfFile.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-VcfFile.R -------------------------------------------------------------------------------- /R/methods-expand.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-expand.R -------------------------------------------------------------------------------- /R/methods-filterVcf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-filterVcf.R -------------------------------------------------------------------------------- /R/methods-genotypeToSnpMatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-genotypeToSnpMatrix.R -------------------------------------------------------------------------------- /R/methods-import.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-import.R -------------------------------------------------------------------------------- /R/methods-locateVariants.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-locateVariants.R -------------------------------------------------------------------------------- /R/methods-predictCoding.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-predictCoding.R -------------------------------------------------------------------------------- /R/methods-readVcf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-readVcf.R -------------------------------------------------------------------------------- /R/methods-scanVcf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-scanVcf.R -------------------------------------------------------------------------------- /R/methods-scanVcfHeader.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-scanVcfHeader.R -------------------------------------------------------------------------------- /R/methods-snpSummary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-snpSummary.R -------------------------------------------------------------------------------- /R/methods-summarizeVariants.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-summarizeVariants.R -------------------------------------------------------------------------------- /R/methods-writeVcf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/methods-writeVcf.R -------------------------------------------------------------------------------- /R/test_VariantAnnotation_package.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/test_VariantAnnotation_package.R -------------------------------------------------------------------------------- /R/use_vep_api.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/R/use_vep_api.R -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/CITATION -------------------------------------------------------------------------------- /inst/extdata/chr22.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/chr22.vcf.gz -------------------------------------------------------------------------------- /inst/extdata/chr22.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/chr22.vcf.gz.tbi -------------------------------------------------------------------------------- /inst/extdata/chr7-sub.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/chr7-sub.vcf.gz -------------------------------------------------------------------------------- /inst/extdata/chr7-sub.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/chr7-sub.vcf.gz.tbi -------------------------------------------------------------------------------- /inst/extdata/ex2.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/ex2.vcf -------------------------------------------------------------------------------- /inst/extdata/gl_chr1.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/gl_chr1.vcf -------------------------------------------------------------------------------- /inst/extdata/h1187-10k.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/h1187-10k.vcf.gz -------------------------------------------------------------------------------- /inst/extdata/h1187-10k.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/h1187-10k.vcf.gz.tbi -------------------------------------------------------------------------------- /inst/extdata/hapmap_exome_chr22.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/hapmap_exome_chr22.vcf.gz -------------------------------------------------------------------------------- /inst/extdata/hapmap_exome_chr22.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/hapmap_exome_chr22.vcf.gz.tbi -------------------------------------------------------------------------------- /inst/extdata/structural.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/extdata/structural.vcf -------------------------------------------------------------------------------- /inst/scripts/test_Rplinkseq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/scripts/test_Rplinkseq.R -------------------------------------------------------------------------------- /inst/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/VarScan_header.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/VarScan_header.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/banded_gvcf.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/banded_gvcf.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/buffer_realloc.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/buffer_realloc.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/ex1-seq1-90.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/ex1-seq1-90.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/expand.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/expand.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/fewer-FORMAT-than-GENO.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/fewer-FORMAT-than-GENO.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/meta_header.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/meta_header.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/missing-FORMAT-metadata-elt.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/missing-FORMAT-metadata-elt.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/mixedStructural.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/mixedStructural.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/multiple_INFO_fields.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/multiple_INFO_fields.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/negative_FORMAT_Number.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/negative_FORMAT_Number.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/no_FORMAT_column.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/no_FORMAT_column.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/no_GENO_row.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/no_GENO_row.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/no_INFO_header.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/no_INFO_header.vcf -------------------------------------------------------------------------------- /inst/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf -------------------------------------------------------------------------------- /inst/unitTests/test_SIFTandPolyPhen.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_SIFTandPolyPhen.R -------------------------------------------------------------------------------- /inst/unitTests/test_ScanVcfParam-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_ScanVcfParam-class.R -------------------------------------------------------------------------------- /inst/unitTests/test_VCF-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_VCF-class.R -------------------------------------------------------------------------------- /inst/unitTests/test_VRanges-class.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_VRanges-class.R -------------------------------------------------------------------------------- /inst/unitTests/test_expand-methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_expand-methods.R -------------------------------------------------------------------------------- /inst/unitTests/test_filterVcf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_filterVcf.R -------------------------------------------------------------------------------- /inst/unitTests/test_genotypeToSnpMatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_genotypeToSnpMatrix.R -------------------------------------------------------------------------------- /inst/unitTests/test_isSNV.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_isSNV.R -------------------------------------------------------------------------------- /inst/unitTests/test_locateVariants-methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_locateVariants-methods.R -------------------------------------------------------------------------------- /inst/unitTests/test_predictCoding-methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_predictCoding-methods.R -------------------------------------------------------------------------------- /inst/unitTests/test_readVcf-methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_readVcf-methods.R -------------------------------------------------------------------------------- /inst/unitTests/test_scanVcf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_scanVcf.R -------------------------------------------------------------------------------- /inst/unitTests/test_snpSummary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_snpSummary.R -------------------------------------------------------------------------------- /inst/unitTests/test_summarizeVariants-methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_summarizeVariants-methods.R -------------------------------------------------------------------------------- /inst/unitTests/test_vcfFields.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_vcfFields.R -------------------------------------------------------------------------------- /inst/unitTests/test_writeVcf-methods.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/inst/unitTests/test_writeVcf-methods.R -------------------------------------------------------------------------------- /man/GLtoGP.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/GLtoGP.Rd -------------------------------------------------------------------------------- /man/PROVEANDb-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/PROVEANDb-class.Rd -------------------------------------------------------------------------------- /man/PolyPhenDb-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/PolyPhenDb-class.Rd -------------------------------------------------------------------------------- /man/PolyPhenDbColumns.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/PolyPhenDbColumns.Rd -------------------------------------------------------------------------------- /man/SIFTDb-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/SIFTDb-class.Rd -------------------------------------------------------------------------------- /man/SIFTDbColumns.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/SIFTDbColumns.Rd -------------------------------------------------------------------------------- /man/ScanVcfParam-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/ScanVcfParam-class.Rd -------------------------------------------------------------------------------- /man/VCF-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/VCF-class.Rd -------------------------------------------------------------------------------- /man/VCFHeader-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/VCFHeader-class.Rd -------------------------------------------------------------------------------- /man/VRanges-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/VRanges-class.Rd -------------------------------------------------------------------------------- /man/VRangesList-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/VRangesList-class.Rd -------------------------------------------------------------------------------- /man/VariantType-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/VariantType-class.Rd -------------------------------------------------------------------------------- /man/VcfFile-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/VcfFile-class.Rd -------------------------------------------------------------------------------- /man/defunct.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/defunct.Rd -------------------------------------------------------------------------------- /man/filterVcf-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/filterVcf-methods.Rd -------------------------------------------------------------------------------- /man/genotypeToSnpMatrix-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/genotypeToSnpMatrix-methods.Rd -------------------------------------------------------------------------------- /man/getTranscriptSeqs-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/getTranscriptSeqs-methods.Rd -------------------------------------------------------------------------------- /man/indexVcf-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/indexVcf-method.Rd -------------------------------------------------------------------------------- /man/isSNV-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/isSNV-methods.Rd -------------------------------------------------------------------------------- /man/locateVariants-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/locateVariants-methods.Rd -------------------------------------------------------------------------------- /man/post_Hs_region.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/post_Hs_region.Rd -------------------------------------------------------------------------------- /man/predictCoding-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/predictCoding-methods.Rd -------------------------------------------------------------------------------- /man/probabilityToSnpMatrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/probabilityToSnpMatrix.Rd -------------------------------------------------------------------------------- /man/readVcf-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/readVcf-methods.Rd -------------------------------------------------------------------------------- /man/scanVcf-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/scanVcf-methods.Rd -------------------------------------------------------------------------------- /man/seqinfo-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/seqinfo-method.Rd -------------------------------------------------------------------------------- /man/snpSummary.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/snpSummary.Rd -------------------------------------------------------------------------------- /man/summarizeVariants-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/summarizeVariants-methods.Rd -------------------------------------------------------------------------------- /man/variant_body.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/variant_body.Rd -------------------------------------------------------------------------------- /man/vep_by_region.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/vep_by_region.Rd -------------------------------------------------------------------------------- /man/writeVcf-methods.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/man/writeVcf-methods.Rd -------------------------------------------------------------------------------- /src/Biostrings_stubs.c: -------------------------------------------------------------------------------- 1 | #include "_Biostrings_stubs.c" 2 | -------------------------------------------------------------------------------- /src/IRanges_stubs.c: -------------------------------------------------------------------------------- 1 | #include "_IRanges_stubs.c" 2 | -------------------------------------------------------------------------------- /src/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/Makevars -------------------------------------------------------------------------------- /src/R_init_VariantAnnotation.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/R_init_VariantAnnotation.c -------------------------------------------------------------------------------- /src/XVector_stubs.c: -------------------------------------------------------------------------------- 1 | #include "_XVector_stubs.c" 2 | -------------------------------------------------------------------------------- /src/dna_hash.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/dna_hash.c -------------------------------------------------------------------------------- /src/dna_hash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/dna_hash.h -------------------------------------------------------------------------------- /src/rle.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/rle.c -------------------------------------------------------------------------------- /src/rle.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/rle.h -------------------------------------------------------------------------------- /src/strhash.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/strhash.c -------------------------------------------------------------------------------- /src/strhash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/strhash.h -------------------------------------------------------------------------------- /src/utilities.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/utilities.c -------------------------------------------------------------------------------- /src/utilities.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/utilities.h -------------------------------------------------------------------------------- /src/vcffile.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/vcffile.c -------------------------------------------------------------------------------- /src/vcffile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/vcffile.h -------------------------------------------------------------------------------- /src/vcftype.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/vcftype.c -------------------------------------------------------------------------------- /src/vcftype.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/vcftype.h -------------------------------------------------------------------------------- /src/writevcf.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/writevcf.c -------------------------------------------------------------------------------- /src/writevcf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/src/writevcf.h -------------------------------------------------------------------------------- /tests/VariantAnnotation_unit_tests.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/tests/VariantAnnotation_unit_tests.R -------------------------------------------------------------------------------- /vignettes/VariantAnnotation.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/vignettes/VariantAnnotation.Rmd -------------------------------------------------------------------------------- /vignettes/bioinformatics.csl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/vignettes/bioinformatics.csl -------------------------------------------------------------------------------- /vignettes/ens.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/vignettes/ens.bib -------------------------------------------------------------------------------- /vignettes/ensemblVEP.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/vignettes/ensemblVEP.Rmd -------------------------------------------------------------------------------- /vignettes/filterVcf.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/vignettes/filterVcf.Rmd -------------------------------------------------------------------------------- /vignettes/filterVcf.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/VariantAnnotation/HEAD/vignettes/filterVcf.bib --------------------------------------------------------------------------------