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