A B C D F G I N O P R S U misc
Rsamtools-package | 'samtools' aligned sequence utilities interface |
asBam | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
asBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
bamDirname<- | Views into a set of BAM files |
bamExperiment | Views into a set of BAM files |
BamFile | Maintain SAM and BAM files |
BamFile-class | Maintain SAM and BAM files |
bamFlag | Parameters for scanning BAM files |
bamFlag<- | Parameters for scanning BAM files |
bamIndicies | Views into a set of BAM files |
bamPaths | Views into a set of BAM files |
bamRanges | Views into a set of BAM files |
bamRanges<- | Views into a set of BAM files |
bamReverseComplement | Parameters for scanning BAM files |
bamReverseComplement<- | Parameters for scanning BAM files |
bamSamples | Views into a set of BAM files |
bamSamples<- | Views into a set of BAM files |
bamSimpleCigar | Parameters for scanning BAM files |
bamSimpleCigar<- | Parameters for scanning BAM files |
bamTag | Parameters for scanning BAM files |
bamTag<- | Parameters for scanning BAM files |
BamViews | Views into a set of BAM files |
BamViews-class | Views into a set of BAM files |
BamViews-method | Views into a set of BAM files |
bamWhat | Parameters for scanning BAM files |
bamWhat<- | Parameters for scanning BAM files |
bamWhich | Parameters for scanning BAM files |
bamWhich<- | Parameters for scanning BAM files |
BcfFile | Manipulate BCF or VCF files. |
BcfFile-class | Manipulate BCF or VCF files. |
bcfGeno | Parameters for scanning VCF / BCF files |
bcfInfo | Parameters for scanning VCF / BCF files |
bcfMode | Manipulate BCF or VCF files. |
bcfTrimEmpty | Parameters for scanning VCF / BCF files |
bcfWhich | Parameters for scanning VCF / BCF files |
bzfile-class | 'samtools' aligned sequence utilities interface |
close.BamFile | Maintain SAM and BAM files |
close.BcfFile | Manipulate BCF or VCF files. |
close.FaFile | Manipulate indexed fasta files. |
countBam | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
countBam-method | Maintain SAM and BAM files |
countBam-method | Views into a set of BAM files |
countBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
countFa | Operations on indexed 'fasta' files. |
countFa-method | Manipulate indexed fasta files. |
countFa-method | Operations on indexed 'fasta' files. |
dim-method | Views into a set of BAM files |
dimnames-method | Views into a set of BAM files |
dimnames<--method | Views into a set of BAM files |
FaFile | Manipulate indexed fasta files. |
FaFile-class | Manipulate indexed fasta files. |
fifo-class | 'samtools' aligned sequence utilities interface |
filterBam | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
filterBam-method | Maintain SAM and BAM files |
filterBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
gzfile-class | 'samtools' aligned sequence utilities interface |
index | A base class for managing file references in Rsamtools |
indexBam | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
indexBam-method | Maintain SAM and BAM files |
indexBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
indexFa | Operations on indexed 'fasta' files. |
indexFa-method | Manipulate indexed fasta files. |
indexFa-method | Operations on indexed 'fasta' files. |
isOpen-method | Maintain SAM and BAM files |
isOpen-method | Manipulate BCF or VCF files. |
isOpen-method | Manipulate indexed fasta files. |
isOpen-method | A base class for managing file references in Rsamtools |
names-method | Views into a set of BAM files |
names<--method | Views into a set of BAM files |
open.BamFile | Maintain SAM and BAM files |
open.BcfFile | Manipulate BCF or VCF files. |
open.FaFile | Manipulate indexed fasta files. |
path | A base class for managing file references in Rsamtools |
pipe-class | 'samtools' aligned sequence utilities interface |
readBamGappedAlignments | GappedAlignments objects |
readBamGappedAlignments-method | Maintain SAM and BAM files |
readBamGappedAlignments-method | Views into a set of BAM files |
readBamGappedAlignments-method | GappedAlignments objects |
readPileup | Import samtools 'pileup' files. |
readPileup-method | Import samtools 'pileup' files. |
Rsamtools | 'samtools' aligned sequence utilities interface |
RsamtoolsFile-class | A base class for managing file references in Rsamtools |
scanBam | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
scanBam-method | Maintain SAM and BAM files |
scanBam-method | Views into a set of BAM files |
scanBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
scanBamFlag | Parameters for scanning BAM files |
scanBamHeader | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
scanBamHeader-method | Maintain SAM and BAM files |
scanBamHeader-method | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
ScanBamParam | Parameters for scanning BAM files |
ScanBamParam-class | Parameters for scanning BAM files |
ScanBamParam-method | Parameters for scanning BAM files |
scanBamWhat | Parameters for scanning BAM files |
scanBcf | Operations on 'VCF' or 'BCF' (variant call) files. |
scanBcf-method | Manipulate BCF or VCF files. |
scanBcf-method | Operations on 'VCF' or 'BCF' (variant call) files. |
scanBcfHeader | Operations on 'VCF' or 'BCF' (variant call) files. |
scanBcfHeader-method | Manipulate BCF or VCF files. |
scanBcfHeader-method | Operations on 'VCF' or 'BCF' (variant call) files. |
ScanBcfParam | Parameters for scanning VCF / BCF files |
ScanBcfParam-class | Parameters for scanning VCF / BCF files |
ScanBcfParam-method | Parameters for scanning VCF / BCF files |
scanFa | Operations on indexed 'fasta' files. |
scanFa-method | Manipulate indexed fasta files. |
scanFa-method | Operations on indexed 'fasta' files. |
scanFaIndex | Operations on indexed 'fasta' files. |
scanFaIndex-method | Manipulate indexed fasta files. |
scanFaIndex-method | Operations on indexed 'fasta' files. |
show-method | Views into a set of BAM files |
show-method | A base class for managing file references in Rsamtools |
show-method | Parameters for scanning BAM files |
show-method | Parameters for scanning VCF / BCF files |
sortBam | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
sortBam-method | Maintain SAM and BAM files |
sortBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files. |
unz-class | 'samtools' aligned sequence utilities interface |
url-class | 'samtools' aligned sequence utilities interface |
[-method | Views into a set of BAM files |