Files in Jiefei-Wang/VariantAnnotation
Annotation of Genetic Variants
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.R
R/AllGenerics.R
R/AllUtilities.R
R/makeVRangesFromGRanges.R
R/methods-CollapsedVCF-class.R
R/methods-ExpandedVCF-class.R
R/methods-PROVEANDb.class.R
R/methods-PolyPhenDb-class.R
R/methods-SIFTDb-class.R
R/methods-ScanVcfParam-class.R
R/methods-VCF-class.R
R/methods-VCFHeader-class.R
R/methods-VRanges-class.R
R/methods-VRangesList-class.R
R/methods-VariantType-class.R
R/methods-VcfFile.R
R/methods-expand.R
R/methods-filterVcf.R
R/methods-genotypeToSnpMatrix.R
R/methods-import.R
R/methods-locateVariants.R
R/methods-predictCoding.R
R/methods-readVcf.R
R/methods-scanVcf.R
R/methods-scanVcfHeader.R
R/methods-snpSummary.R
R/methods-summarizeVariants.R
R/methods-writeVcf.R
R/test_VariantAnnotation_package.R
inst/CITATION
inst/extdata/chr22.vcf.gz
inst/extdata/chr22.vcf.gz.tbi
inst/extdata/chr7-sub.vcf.gz
inst/extdata/chr7-sub.vcf.gz.tbi
inst/extdata/ex2.vcf
inst/extdata/gl_chr1.vcf
inst/extdata/h1187-10k.vcf.gz
inst/extdata/h1187-10k.vcf.gz.tbi
inst/extdata/hapmap_exome_chr22.vcf.gz
inst/extdata/hapmap_exome_chr22.vcf.gz.tbi
inst/extdata/structural.vcf
inst/scripts/test_Rplinkseq.R
inst/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf
inst/unitTests/cases/VarScan_header.vcf
inst/unitTests/cases/banded_gvcf.vcf
inst/unitTests/cases/buffer_realloc.vcf
inst/unitTests/cases/ex1-seq1-90.vcf
inst/unitTests/cases/expand.vcf
inst/unitTests/cases/fewer-FORMAT-than-GENO.vcf
inst/unitTests/cases/meta_header.vcf
inst/unitTests/cases/missing-FORMAT-metadata-elt.vcf
inst/unitTests/cases/mixedStructural.vcf
inst/unitTests/cases/multiple_INFO_fields.vcf
inst/unitTests/cases/negative_FORMAT_Number.vcf
inst/unitTests/cases/no_FORMAT_column.vcf
inst/unitTests/cases/no_GENO_row.vcf
inst/unitTests/cases/no_INFO_header.vcf
inst/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf
inst/unitTests/test_SIFTandPolyPhen.R
inst/unitTests/test_ScanVcfParam-class.R
inst/unitTests/test_VCF-class.R
inst/unitTests/test_VRanges-class.R
inst/unitTests/test_expand-methods.R
inst/unitTests/test_filterVcf.R
inst/unitTests/test_genotypeToSnpMatrix.R
inst/unitTests/test_isSNV.R
inst/unitTests/test_locateVariants-methods.R
inst/unitTests/test_predictCoding-methods.R
inst/unitTests/test_readVcf-methods.R
inst/unitTests/test_scanVcf.R
inst/unitTests/test_snpSummary.R
inst/unitTests/test_summarizeVariants-methods.R
inst/unitTests/test_vcfFields.R
inst/unitTests/test_writeVcf-methods.R
man/GLtoGP.Rd
man/PROVEANDb-class.Rd
man/PolyPhenDb-class.Rd
man/PolyPhenDbColumns.Rd
man/SIFTDb-class.Rd
man/SIFTDbColumns.Rd
man/ScanVcfParam-class.Rd
man/VCF-class.Rd
man/VCFHeader-class.Rd
man/VRanges-class.Rd
man/VRangesList-class.Rd
man/VariantType-class.Rd
man/VcfFile-class.Rd
man/defunct.Rd
man/filterVcf-methods.Rd
man/genotypeToSnpMatrix-methods.Rd
man/getTranscriptSeqs-methods.Rd
man/indexVcf-method.Rd
man/isSNV-methods.Rd
man/locateVariants-methods.Rd
man/predictCoding-methods.Rd
man/probabilityToSnpMatrix.Rd
man/readVcf-methods.Rd
man/scanVcf-methods.Rd
man/seqinfo-method.Rd
man/snpSummary.Rd
man/summarizeVariants-methods.Rd
man/writeVcf-methods.Rd
src/Biostrings_stubs.c
src/IRanges_stubs.c
src/Makevars
src/R_init_VariantAnnotation.c
src/XVector_stubs.c
src/dna_hash.c
src/dna_hash.h
src/rle.c
src/rle.h
src/strhash.c
src/strhash.h
src/utilities.c
src/utilities.h
src/vcffile.c
src/vcffile.h
src/vcftype.c
src/vcftype.h
src/writevcf.c
src/writevcf.h
tests/VariantAnnotation_unit_tests.R
vignettes/VariantAnnotation.Rnw
vignettes/filterVcf.Rnw
vignettes/filterVcf.bib
