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 |