# Import aligned BAM file format sequences into R / Bioconductor

## Documentation for package ‘Rsamtools’ version 1.0.8

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

Rsamtools-package | 'samtools' aligned sequence utilities interface
bamDirname<- | Views into a set of BAM files
bamExperiment | Views into a set of 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
countBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
countBam-method | Views into a set of BAM files
countBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) 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
filterBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
filterBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexBam | Import, count, index, and other operations on 'BAM' (binary alignment) files.
indexBam-method | Import, count, index, and other operations on 'BAM' (binary alignment) files.
names-method | Views into a set of BAM files
names<--method | Views into a set of BAM files
readBamGappedAlignments | GappedAlignments objects
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
scanBam | Import, count, index, and other operations on 'BAM' (binary alignment) 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 | 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
show-method | Views into a set of BAM files
show-method | Parameters for scanning BAM files
[-method | Views into a set of BAM files