Compress and index tabix-compatible files.
Apply a user-provided function to calculate pile-up statistics across
multiple BAM files.
Manipulate BCF files.
Manipulate indexed fasta files.
Deprecated functions
Parameters for creating pileups from BAM files
Retrieve sequence names defined in a tabix file.
Rsamtools Deprecated and Defunct
Views into a set of BAM files
Maintain and use BAM files
Represent BAM files for pileup summaries.
A base class for managing file references in Rsamtools
A base class for managing lists of Rsamtools file references
Operations on `BCF' files.
Import samtools 'pileup' files.
'samtools' aligned sequence utilities interface
Use filters and output formats to calculate pile-up statistics for a
BAM file.
Import, count, index, filter, sort, and merge `BAM' (binary alignment)
files.
Parameters for scanning BAM files
Group the records of a BAM file based on their flag bits and count
the number of records in each group
File compression for tabix (bgzip) and fasta (razip) files.
Operations on `tabix' (indexed, tab-delimited) files.
Retrieve sequence names defined in a tabix file.
Operations on indexed 'fasta' files.
Parameters for scanning BCF files
Manipulate tabix indexed tab-delimited files.
Quickly test if a BAM file has paired end reads