Parameters for creating pileups from BAM files
Maintain and use BAM files
Views into a set of BAM files
Manipulate BCF files.
Manipulate indexed fasta 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
Parameters for scanning BAM files
Parameters for scanning BCF files
Manipulate tabix indexed tab-delimited files.
Apply a user-provided function to calculate pile-up statistics across multiple BAM files.
Rsamtools Deprecated and Defunct
Deprecated functions
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 samtools 'pileup' files.
Import, count, index, filter, sort, and merge 'BAM' (binary alignment) files.
Operations on 'BCF' files.
Operations on indexed 'fasta' files.
Operations on 'tabix' (indexed, tab-delimited) files.
Retrieve sequence names defined in a tabix file.
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.