/usr/lib/R/site-library/VariantAnnotation/help/AnIndex is in r-bioc-variantannotation 1.20.2-1+b1.
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AllVariants-class VariantType-class
alt VCF-class
alt,VCF-method VCF-class
alt,VRanges-method VRanges-class
alt<- VCF-class
alt<-,CollapsedVCF,CharacterList-method VCF-class
alt<-,CollapsedVCF,DNAStringSetList-method VCF-class
alt<-,ExpandedVCF,character-method VCF-class
alt<-,ExpandedVCF,DNAStringSet-method VCF-class
alt<-,VRanges,ANY-method VRanges-class
altDepth VRanges-class
altDepth,VRanges-method VRanges-class
altDepth<- VRanges-class
altDepth<-,VRanges-method VRanges-class
altFraction VRanges-class
altFraction,VRanges-method VRanges-class
asVCF VRanges-class
asVCF,VRanges-method VRanges-class
called VRanges-class
called,VRanges-method VRanges-class
cbind,VCF-method VCF-class
characterOrRle-class VRanges-class
characterRle-class VRanges-class
class:CollapsedVCF VCF-class
class:CompressedVRangesList VRangesList-class
class:ExpandedVCF VCF-class
class:PolyPhenDb PolyPhenDb-class
class:PROVEANDb PROVEANDb-class
class:SIFTDb SIFTDb-class
class:SimpleVRangesList VRangesList-class
class:VCF VCF-class
class:VRanges VRanges-class
class:VRangesList VRangesList-class
CodingVariants VariantType-class
CodingVariants-class VariantType-class
coerce,GRanges,VRanges-method VRanges-class
coerce,VCF,VRanges-method VRanges-class
coerce,VRanges,VCF-method VRanges-class
CollapsedVCF VCF-class
CollapsedVCF-class VCF-class
columns,PolyPhenDb-method PolyPhenDb-class
columns,PROVEANDb-method PROVEANDb-class
columns,SIFTDb-method SIFTDb-class
complexRle-class VRanges-class
CompressedVRangesList-class VRangesList-class
contig VCFHeader-class
contig,VCFHeader-method VCFHeader-class
dbSNPFilter defunct
dimnames<-,VCF,list-method VCF-class
downstream VariantType-class
downstream,AllVariants-method VariantType-class
downstream,IntergenicVariants-method VariantType-class
downstream,PromoterVariants-method VariantType-class
downstream<- VariantType-class
downstream<-,AllVariants-method VariantType-class
downstream<-,IntergenicVariants-method VariantType-class
downstream<-,PromoterVariants-method VariantType-class
duplicateRSID PolyPhenDb-class
expand,CollapsedVCF-method VCF-class
expand,ExpandedVCF-method VCF-class
ExpandedVCF VCF-class
ExpandedVCF-class VCF-class
factorOrRle-class VRanges-class
factorRle-class VRanges-class
filt VCF-class
filt,VCF-method VCF-class
filt<- VCF-class
filt<-,VCF,character-method VCF-class
filterVcf filterVcf-methods
filterVcf,character-method filterVcf-methods
filterVcf,TabixFile-method filterVcf-methods
FiveUTRVariants VariantType-class
FiveUTRVariants-class VariantType-class
fixed VCF-class
fixed,VCF-method VCF-class
fixed,VCFHeader-method VCFHeader-class
fixed<- VCF-class
fixed<-,VCF,DataFrame-method VCF-class
fixed<-,VCFHeader,DataFrameList-method VCFHeader-class
geno VCF-class
geno,VCF,ANY-method VCF-class
geno,VCF,character-method VCF-class
geno,VCF,numeric-method VCF-class
geno,VCF-method VCF-class
geno,VCFHeader,ANY-method VCF-class
geno,VCFHeader-method VCFHeader-class
geno<- VCF-class
geno<-,VCF,character,matrix-method VCF-class
geno<-,VCF,missing,matrix-method VCF-class
geno<-,VCF,missing,SimpleList-method VCF-class
geno<-,VCF,numeric,matrix-method VCF-class
geno<-,VCFHeader,missing,DataFrame-method VCFHeader-class
genome,VCF-method VCF-class
genotypeCodesToNucleotides VCF-class
genotypeToSnpMatrix genotypeToSnpMatrix-methods
genotypeToSnpMatrix,array-method genotypeToSnpMatrix-methods
genotypeToSnpMatrix,CollapsedVCF-method genotypeToSnpMatrix-methods
getTranscriptSeqs getTranscriptSeqs-methods
getTranscriptSeqs,GRanges,FaFile-method getTranscriptSeqs-methods
getTranscriptSeqs,GRangesList,ANY-method getTranscriptSeqs-methods
getTranscriptSeqs,GRangesList,BSgenome-method getTranscriptSeqs-methods
getTranscriptSeqs,GRangesList,FaFile-method getTranscriptSeqs-methods
GLtoGP GLtoGP
hardFilters VRanges-class
hardFilters,VRanges-method VRanges-class
hardFilters<- VRanges-class
hardFilters<-,VRanges-method VRanges-class
header VCFHeader-class
header,VCF-method VCF-class
header,VCFHeader-method VCFHeader-class
header<- VCF-class
header<-,VCF,VCFHeader-method VCF-class
import,VcfFile,ANY,ANY-method readVcf-methods
info VCF-class
info,VCF-method VCF-class
info,VCFHeader-method VCFHeader-class
info<- VCF-class
info<-,VCF,DataFrame-method VCF-class
info<-,VCFHeader,DataFrame-method VCFHeader-class
integerOrRle-class VRanges-class
integerRle-class VRanges-class
intergenic VariantType-class
intergenic,AllVariants-method VariantType-class
intergenic<- VariantType-class
intergenic<-,AllVariants-method VariantType-class
IntergenicVariants VariantType-class
IntergenicVariants-class VariantType-class
IntronVariants VariantType-class
IntronVariants-class VariantType-class
isDeletion isSNV-methods
isDeletion,CollapsedVCF-method isSNV-methods
isDeletion,ExpandedVCF-method isSNV-methods
isDeletion,VRanges-method isSNV-methods
isDelins isSNV-methods
isDelins,CollapsedVCF-method isSNV-methods
isDelins,ExpandedVCF-method isSNV-methods
isDelins,VRanges-method isSNV-methods
isIndel isSNV-methods
isIndel,CollapsedVCF-method isSNV-methods
isIndel,ExpandedVCF-method isSNV-methods
isIndel,VRanges-method isSNV-methods
isInsertion isSNV-methods
isInsertion,CollapsedVCF-method isSNV-methods
isInsertion,ExpandedVCF-method isSNV-methods
isInsertion,VRanges-method isSNV-methods
isSNV isSNV-methods
isSNV,CollapsedVCF-method isSNV-methods
isSNV,ExpandedVCF-method isSNV-methods
isSNV,VRanges-method isSNV-methods
isSubstitution isSNV-methods
isSubstitution,CollapsedVCF-method isSNV-methods
isSubstitution,ExpandedVCF-method isSNV-methods
isSubstitution,VRanges-method isSNV-methods
isTransition isSNV-methods
isTransition,CollapsedVCF-method isSNV-methods
isTransition,ExpandedVCF-method isSNV-methods
isTransition,VRanges-method isSNV-methods
keys,PolyPhenDb-method PolyPhenDb-class
keys,PROVEANDb-method PROVEANDb-class
keys,SIFTDb-method SIFTDb-class
keytypes,PROVEANDb-method PROVEANDb-class
locateVariants locateVariants-methods
locateVariants,GRanges,GRangesList,AllVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,CodingVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,FiveUTRVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,IntergenicVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,IntronVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,PromoterVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,SpliceSiteVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,ThreeUTRVariants-method locateVariants-methods
locateVariants,GRanges,GRangesList,VariantType-method locateVariants-methods
locateVariants,GRanges,TxDb,AllVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,CodingVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,FiveUTRVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,IntergenicVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,IntronVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,PromoterVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,SpliceSiteVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,ThreeUTRVariants-method locateVariants-methods
locateVariants,GRanges,TxDb,VariantType-method locateVariants-methods
locateVariants,Ranges,GRangesList,VariantType-method locateVariants-methods
locateVariants,Ranges,TxDb,VariantType-method locateVariants-methods
locateVariants,VCF,GRangesList,VariantType-method locateVariants-methods
locateVariants,VCF,TxDb,VariantType-method locateVariants-methods
logicalRle-class VRanges-class
makeVRangesFromGRanges VRanges-class
match,VRanges,VRanges-method VRanges-class
MatrixToSnpMatrix defunct
mcols<-,VCF,DataFrame-method VCF-class
meta VCFHeader-class
meta,VCFHeader-method VCFHeader-class
meta<- VCFHeader-class
meta<-,VCFHeader,DataFrame-method VCFHeader-class
meta<-,VCFHeader,DataFrameList-method VCFHeader-class
metadata,PolyPhenDb-method PolyPhenDb-class
metadata,SIFTDb-method SIFTDb-class
numericRle-class VRanges-class
PLtoGP GLtoGP
PolyPhen PolyPhenDb-class
PolyPhenDb PolyPhenDb-class
PolyPhenDb-class PolyPhenDb-class
PolyPhenDbColumns PolyPhenDbColumns
predictCoding predictCoding-methods
predictCoding,CollapsedVCF,TxDb,ANY,missing-method predictCoding-methods
predictCoding,ExpandedVCF,TxDb,ANY,missing-method predictCoding-methods
predictCoding,GRanges,TxDb,ANY,DNAStringSet-method predictCoding-methods
predictCoding,Ranges,TxDb,ANY,DNAStringSet-method predictCoding-methods
predictCoding,VRanges,TxDb,ANY,missing-method predictCoding-methods
probabilityToSnpMatrix probabilityToSnpMatrix
promoter VariantType-class
promoter,AllVariants-method VariantType-class
promoter<- VariantType-class
promoter<-,AllVariants-method VariantType-class
PromoterVariants VariantType-class
PromoterVariants-class VariantType-class
PROVEAN PROVEANDb-class
PROVEANDb PROVEANDb-class
PROVEANDb-class PROVEANDb-class
qual VCF-class
qual,VCF-method VCF-class
qual<- VCF-class
qual<-,VCF,numeric-method VCF-class
rawRle-class VRanges-class
rbind,VCF-method VCF-class
readGeno readVcf-methods
readGT readVcf-methods
readInfo readVcf-methods
readVcf readVcf-methods
readVcf,character,ANY-method readVcf-methods
readVcf,character,missing-method readVcf-methods
readVcf,TabixFile,GRanges-method readVcf-methods
readVcf,TabixFile,GRangesList-method readVcf-methods
readVcf,TabixFile,missing-method readVcf-methods
readVcf,TabixFile,RangesList-method readVcf-methods
readVcf,TabixFile,ScanVcfParam-method readVcf-methods
readVcfAsVRanges VRanges-class
readVcfLongForm defunct
readVcfLongForm,character,character,missing-method defunct
readVcfLongForm,character,character,ScanVcfParam-method defunct
readVcfLongForm,character,missing,missing-method defunct
readVcfLongForm,TabixFile,character,GRanges-method defunct
readVcfLongForm,TabixFile,character,missing-method defunct
readVcfLongForm,TabixFile,character,RangesList-method defunct
readVcfLongForm,TabixFile,character,ScanVcfParam-method defunct
ref VCF-class
ref,VCF-method VCF-class
ref,VRanges-method VRanges-class
ref<- VCF-class
ref<-,VCF,DNAStringSet-method VCF-class
ref<-,VRanges,ANY-method VRanges-class
refDepth VRanges-class
refDepth,VRanges-method VRanges-class
refDepth<- VRanges-class
refDepth<-,VRanges-method VRanges-class
reference VCFHeader-class
reference,VCFHeader-method VCFHeader-class
refLocsToLocalLocs defunct
refLocsToLocalLocs,GRanges,missing,GRangesList-method defunct
refLocsToLocalLocs,GRanges,TxDb,missing-method defunct
regionFilter defunct
resetFilter VRanges-class
restrictToSNV defunct
rowRanges,VCF-method VCF-class
rowRanges<-,VCF-method VCF-class
sampleNames,VRanges-method VRanges-class
sampleNames<-,VRanges,ANY-method VRanges-class
samples VCFHeader-class
samples,VCFHeader-method VCFHeader-class
scanVcf scanVcf-methods
scanVcf,character,missing-method scanVcf-methods
scanVcf,character,ScanVcfParam-method scanVcf-methods
scanVcf,connection,missing-method scanVcf-methods
scanVcf,TabixFile,GRanges-method scanVcf-methods
scanVcf,TabixFile,missing-method scanVcf-methods
scanVcf,TabixFile,RangesList-method scanVcf-methods
scanVcf,TabixFile,ScanVcfParam-method scanVcf-methods
scanVcfHeader scanVcf-methods
scanVcfHeader,character-method scanVcf-methods
scanVcfHeader,TabixFile-method scanVcf-methods
ScanVcfParam ScanVcfParam-class
ScanVcfParam,ANY-method ScanVcfParam-class
ScanVcfParam,missing-method ScanVcfParam-class
ScanVcfParam-class ScanVcfParam-class
select,PolyPhenDb-method PolyPhenDb-class
select,PROVEANDb-method PROVEANDb-class
select,SIFTDb-method SIFTDb-class
seqinfo,VCFHeader-method VCFHeader-class
seqlevels,VCF-method VCF-class
show,AllVariants-method VariantType-class
show,CollapsedVCF-method VCF-class
show,ExpandedVCF-method VCF-class
show,PromoterVariants-method VariantType-class
show,VariantType-method VariantType-class
show,VCF-method VCF-class
show,VCFHeader-method VCFHeader-class
SIFT SIFTDb-class
SIFTDb SIFTDb-class
SIFTDb-class SIFTDb-class
SIFTDbColumns SIFTDbColumns
SimpleVRangesList-class VRangesList-class
SnpMatrixToVCF VCF-class
snpSummary snpSummary
snpSummary,CollapsedVCF-method snpSummary
softFilter VRanges-class
softFilterMatrix VRanges-class
softFilterMatrix,VRanges-method VRanges-class
softFilterMatrix<- VRanges-class
softFilterMatrix<-,VRanges-method VRanges-class
SpliceSiteVariants VariantType-class
SpliceSiteVariants-class VariantType-class
stackSamples VRangesList-class
stackSamples,VRangesList-method VRangesList-class
strand,VCF-method VCF-class
strand<-,VCF,ANY-method VCF-class
summarizeVariants summarizeVariants-methods
summarizeVariants,GRangesList,VCF,function-method summarizeVariants-methods
summarizeVariants,GRangesList,VCF,VariantType-method summarizeVariants-methods
summarizeVariants,TxDb,VCF,CodingVariants-method summarizeVariants-methods
summarizeVariants,TxDb,VCF,FiveUTRVariants-method summarizeVariants-methods
summarizeVariants,TxDb,VCF,IntronVariants-method summarizeVariants-methods
summarizeVariants,TxDb,VCF,PromoterVariants-method summarizeVariants-methods
summarizeVariants,TxDb,VCF,SpliceSiteVariants-method summarizeVariants-methods
summarizeVariants,TxDb,VCF,ThreeUTRVariants-method summarizeVariants-methods
tabulate VRanges-class
tabulate,VRanges-method VRanges-class
ThreeUTRVariants VariantType-class
ThreeUTRVariants-class VariantType-class
totalDepth VRanges-class
totalDepth,VRanges-method VRanges-class
totalDepth<- VRanges-class
totalDepth<-,VRanges-method VRanges-class
upstream VariantType-class
upstream,AllVariants-method VariantType-class
upstream,IntergenicVariants-method VariantType-class
upstream,PromoterVariants-method VariantType-class
upstream<- VariantType-class
upstream<-,AllVariants-method VariantType-class
upstream<-,IntergenicVariants-method VariantType-class
upstream<-,PromoterVariants-method VariantType-class
VariantAnnotation-defunct defunct
VariantType-class VariantType-class
VCF VCF-class
VCF-class VCF-class
VcfFile VcfFile-class
VcfFile-class VcfFile-class
VcfFileList VcfFile-class
VcfFileList-class VcfFile-class
vcfFixed ScanVcfParam-class
vcfFixed<- ScanVcfParam-class
vcfGeno ScanVcfParam-class
vcfGeno<- ScanVcfParam-class
VCFHeader VCFHeader-class
VCFHeader-class VCFHeader-class
vcfInfo ScanVcfParam-class
vcfInfo<- ScanVcfParam-class
vcfSamples ScanVcfParam-class
vcfSamples<- ScanVcfParam-class
vcfTrimEmpty ScanVcfParam-class
vcfTrimEmpty<- ScanVcfParam-class
vcfWhich ScanVcfParam-class
vcfWhich<- ScanVcfParam-class
VRanges VRanges-class
VRanges-class VRanges-class
VRangesList VRangesList-class
VRangesList-class VRangesList-class
VRangesScanVcfParam defunct
writeVcf writeVcf-methods
writeVcf,VCF,character-method writeVcf-methods
writeVcf,VCF,connection-method writeVcf-methods
writeVcf,VRanges,ANY-method VRanges-class
[,VCF,ANY,ANY-method VCF-class
[,VCF-method VCF-class
[<-,VCF,ANY,ANY,VCF-method VCF-class
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