Man pages for Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
| applyPileups | Apply a user-provided function to calculate pile-up... |
| ApplyPileupsParam-class | Parameters for creating pileups from BAM files |
| BamFile-class | Maintain and use BAM files |
| BamViews-class | Views into a set of BAM files |
| BcfFile-class | Manipulate BCF files. |
| defunct | Rsamtools Deprecated and Defunct |
| deprecated | Deprecated functions |
| FaFile-class | Manipulate indexed fasta files. |
| headerTabix | Retrieve sequence names defined in a tabix file. |
| indexTabix | Compress and index tabix-compatible files. |
| pileup | Use filters and output formats to calculate pile-up... |
| PileupFiles-class | Represent BAM files for pileup summaries. |
| quickBamFlagSummary | Group the records of a BAM file based on their flag bits and... |
| readPileup | Import samtools 'pileup' files. |
| RsamtoolsFile-class | A base class for managing file references in Rsamtools |
| RsamtoolsFileList-class | A base class for managing lists of Rsamtools file references |
| Rsamtools-package | 'samtools' aligned sequence utilities interface |
| scanBam | Import, count, index, filter, sort, and merge 'BAM' (binary... |
| ScanBamParam-class | Parameters for scanning BAM files |
| scanBcf | Operations on 'BCF' files. |
| ScanBcfParam-class | Parameters for scanning BCF files |
| scanFa | Operations on indexed 'fasta' files. |
| scanTabix | Operations on 'tabix' (indexed, tab-delimited) files. |
| seqnamesTabix | Retrieve sequence names defined in a tabix file. |
| TabixFile-class | Manipulate tabix indexed tab-delimited files. |
| testPairedEndBam | Quickly test if a BAM file has paired end reads |
| zip | File compression for tabix (bgzip) and fasta (razip) files.... |
