A B C D F G H I N O P R S T U V Y misc
Rsamtools-package | 'samtools' aligned sequence utilities interface |
applyPileups | Create summary pile-up statistics across multiple BAM files. |
applyPileups-method | Represent BAM files for pileup summaries. |
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. |
asBcf | Operations on 'VCF' or 'BCF' (variant call) files. |
asBcf-method | Operations on 'VCF' or 'BCF' (variant call) 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 |
BamFileList | Maintain SAM and BAM files |
BamFileList-class | Maintain SAM and BAM files |
bamFlag | Parameters for scanning BAM files |
bamFlag<- | Parameters for scanning BAM files |
bamFlagAND | Parameters for scanning BAM files |
bamFlagAsBitMatrix | Parameters for scanning BAM files |
bamFlagTest | 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 |
bamWhich<--method | Parameters for scanning BAM files |
BcfFile | Manipulate BCF or VCF files. |
BcfFile-class | Manipulate BCF or VCF files. |
BcfFileList | Manipulate BCF or VCF files. |
BcfFileList-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 |
bgzip | File compression for tabix (bgzip) and fasta (razip) files. |
bgzipTabix | File compression for tabix (bgzip) and fasta (razip) 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. |
close.PileupFiles | Represent BAM files for pileup summaries. |
close.RsamtoolsFileList | A base class for managing lists of Rsamtools file references |
close.TabixFile | Manipulate tabix indexed tab-delimited 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. |
FaFileList | Manipulate indexed fasta files. |
FaFileList-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. |
getSeq-method | Manipulate indexed fasta files. |
gzfile-class | 'samtools' aligned sequence utilities interface |
headerTabix | Retrieve sequence names defined in a tabix file. |
headerTabix-method | Manipulate tabix indexed tab-delimited files. |
headerTabix-method | Retrieve sequence names defined in a tabix file. |
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. |
indexBcf | Operations on 'VCF' or 'BCF' (variant call) files. |
indexBcf-method | Manipulate BCF or VCF files. |
indexBcf-method | Operations on 'VCF' or 'BCF' (variant call) files. |
indexFa | Operations on indexed 'fasta' files. |
indexFa-method | Manipulate indexed fasta files. |
indexFa-method | Operations on indexed 'fasta' files. |
indexTabix | Compress and index tabix-compatible files. |
isOpen-method | Maintain SAM and BAM files |
isOpen-method | Manipulate BCF or VCF files. |
isOpen-method | Manipulate indexed fasta files. |
isOpen-method | Represent BAM files for pileup summaries. |
isOpen-method | A base class for managing file references in Rsamtools |
isOpen-method | A base class for managing lists of Rsamtools file references |
isOpen-method | Manipulate tabix indexed tab-delimited files. |
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. |
open.PileupFiles | Represent BAM files for pileup summaries. |
open.RsamtoolsFileList | A base class for managing lists of Rsamtools file references |
open.TabixFile | Manipulate tabix indexed tab-delimited files. |
path | A base class for managing file references in Rsamtools |
path-method | A base class for managing file references in Rsamtools |
path-method | A base class for managing lists of Rsamtools file references |
PileupFiles | Represent BAM files for pileup summaries. |
PileupFiles-class | Represent BAM files for pileup summaries. |
PileupFiles-method | Represent BAM files for pileup summaries. |
PileupParam | Parameters for creating pileups from BAM files |
PileupParam-class | Parameters for creating pileups from BAM files |
pipe-class | 'samtools' aligned sequence utilities interface |
plpFiles | Represent BAM files for pileup summaries. |
plpFlag | Parameters for creating pileups from BAM files |
plpFlag<- | Parameters for creating pileups from BAM files |
plpMaxDepth | Parameters for creating pileups from BAM files |
plpMaxDepth<- | Parameters for creating pileups from BAM files |
plpMinBaseQuality | Parameters for creating pileups from BAM files |
plpMinBaseQuality<- | Parameters for creating pileups from BAM files |
plpMinDepth | Parameters for creating pileups from BAM files |
plpMinDepth<- | Parameters for creating pileups from BAM files |
plpMinMapQuality | Parameters for creating pileups from BAM files |
plpMinMapQuality<- | Parameters for creating pileups from BAM files |
plpParam | Represent BAM files for pileup summaries. |
plpWhat | Parameters for creating pileups from BAM files |
plpWhat<- | Parameters for creating pileups from BAM files |
plpWhich | Parameters for creating pileups from BAM files |
plpWhich<- | Parameters for creating pileups from BAM files |
plpYieldAll | Parameters for creating pileups from BAM files |
plpYieldAll<- | Parameters for creating pileups from BAM files |
plpYieldBy | Parameters for creating pileups from BAM files |
plpYieldBy<- | Parameters for creating pileups from BAM files |
plpYieldSize | Parameters for creating pileups from BAM files |
plpYieldSize<- | Parameters for creating pileups from BAM files |
razip | File compression for tabix (bgzip) and fasta (razip) files. |
readBamGappedAlignments | Reading GappedAlignments or GappedReads objects from a BAM file |
readBamGappedAlignments-method | Maintain SAM and BAM files |
readBamGappedAlignments-method | Views into a set of BAM files |
readBamGappedAlignments-method | Reading GappedAlignments or GappedReads objects from a BAM file |
readBamGappedReads | Reading GappedAlignments or GappedReads objects from a BAM file |
readBamGappedReads-method | Maintain SAM and BAM files |
readBamGappedReads-method | Reading GappedAlignments or GappedReads objects from a BAM file |
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 |
RsamtoolsFileList | A base class for managing lists of Rsamtools file references |
RsamtoolsFileList-class | A base class for managing lists of Rsamtools file references |
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 |
ScanBVcfParam-class | 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. |
scanTabix | Operations on 'tabix' (indexed, tab-delimited) files. |
scanTabix-method | Manipulate tabix indexed tab-delimited files. |
scanTabix-method | Operations on 'tabix' (indexed, tab-delimited) files. |
scanVcf | Operations on 'VCF' or 'BCF' (variant call) files. |
scanVcf-method | Manipulate tabix indexed tab-delimited files. |
scanVcf-method | Operations on 'VCF' or 'BCF' (variant call) files. |
scanVcfHeader | Operations on 'VCF' or 'BCF' (variant call) files. |
scanVcfHeader-method | Manipulate tabix indexed tab-delimited files. |
scanVcfHeader-method | Operations on 'VCF' or 'BCF' (variant call) files. |
ScanVcfParam | Parameters for scanning VCF / BCF files |
ScanVcfParam-class | Parameters for scanning VCF / BCF files |
ScanVcfParam-method | Parameters for scanning VCF / BCF files |
seqinfo-method | Maintain SAM and BAM files |
seqnamesTabix | Retrieve sequence names defined in a tabix file. |
seqnamesTabix-method | Manipulate tabix indexed tab-delimited files. |
seqnamesTabix-method | Retrieve sequence names defined in a tabix file. |
show-method | Views into a set of BAM files |
show-method | Represent BAM files for pileup summaries. |
show-method | Parameters for creating pileups from 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. |
summarizeOverlaps-method | Maintain SAM and BAM files |
summarizeOverlaps-method | Views into a set of BAM files |
TabixFile | Manipulate tabix indexed tab-delimited files. |
TabixFile-class | Manipulate tabix indexed tab-delimited files. |
TabixFileList | Manipulate tabix indexed tab-delimited files. |
TabixFileList-class | Manipulate tabix indexed tab-delimited files. |
unpackVcf | Operations on 'VCF' or 'BCF' (variant call) files. |
unpackVcf-method | Operations on 'VCF' or 'BCF' (variant call) files. |
unz-class | 'samtools' aligned sequence utilities interface |
url-class | 'samtools' aligned sequence utilities interface |
vcfGeno | Parameters for scanning VCF / BCF files |
vcfInfo | Parameters for scanning VCF / BCF files |
vcfTrimEmpty | Parameters for scanning VCF / BCF files |
vcfWhich | Parameters for scanning VCF / BCF files |
yieldTabix | Yield records from a stream of records contained in a tabix file. |
yieldTabix-method | Manipulate tabix indexed tab-delimited files. |
[-method | Views into a set of BAM files |