Parameters for creating pileups from BAM files
Represent BAM files for pileup summaries.
'samtools' aligned sequence utilities interface
A base class for managing file references in Rsamtools
A base class for managing lists of Rsamtools file references
Manipulate tabix indexed tab-delimited files.
Apply a user-provided function to calculate pile-up statistics across multiple BAM files.
Retrieve sequence names defined in a tabix file.
Compress and index tabix-compatible files.
Use filters and output formats to calculate pile-up statistics for a BAM file.
Group the records of a BAM file based on their flag bits and count the number of records in each group
Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
Operations on 'tabix' (indexed, tab-delimited) files.
Quickly test if a BAM file has paired end reads
File compression for tabix (bgzip) and fasta (razip) files. IMPORTANT NOTE: Starting with Rsamtools 1.99.0 (Bioconductor 3.9), 'razip()' is defunct. Please use 'bgzip()' instead.