Last data update: 2014.03.03
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Cran Task View
BiocViews
SMO (statistical methods ontology)
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ApplyPileupsParam
(Package: Rsamtools ) :
Parameters for creating pileups from BAM files
ApplyPileupsParam() to create a parameter object influencing what fields and which records are used to calculate pile-ups, and to influence the values returned.
● Data Source:
BioConductor
BamFile
(Package: Rsamtools ) :
Maintain and use BAM files
BamFile() to create a reference to a BAM file (and optionally its index). The reference remains open across calls to methods, avoiding costly index re-loading.
● Data Source:
BioConductor
BamViews
(Package: Rsamtools ) :
Views into a set of BAM files
BamViews() to reference a set of disk-based BAM files to be processed (e.g., queried using scanBam) as a single ‘experiment’.
● Data Source:
BioConductor
BcfFile
(Package: Rsamtools ) :
Manipulate BCF files.
BcfFile() to create a reference to a BCF (and optionally its index). The reference remains open across calls to methods, avoiding costly index re-loading.
● Data Source:
BioConductor
FaFile
(Package: Rsamtools ) :
Manipulate indexed fasta files.
FaFile() to create a reference to an indexed fasta file. The reference remains open across calls to methods, avoiding costly index re-loading.
● Data Source:
BioConductor
PileupFiles
(Package: Rsamtools ) :
Represent BAM files for pileup summaries.
PileupFiles() to create a reference to a BAM files (and their indicies), to be used for calculating pile-up summaries.
● Data Source:
BioConductor
This package provides facilities for parsing samtools BAM (binary) files representing aligned sequences.
● Data Source:
BioConductor
RsamtoolsFile
(Package: Rsamtools ) :
A base class for managing file references in Rsamtools
RsamtoolsFile is a base class for managing file references in Rsamtools ; it is not intended for direct use by users – see, e.g., BamFile.
● Data Source:
BioConductor
RsamtoolsFileList
(Package: Rsamtools ) :
A base class for managing lists of Rsamtools file references
RsamtoolsFileList is a base class for managing lists of file references in Rsamtools ; it is not intended for direct use – see, e.g., BamFileList.
● Data Source:
BioConductor
ScanBamParam
(Package: Rsamtools ) :
Parameters for scanning BAM files
ScanBamParam() to create a parameter object influencing what fields and which records are imported from a (binary) BAM file. Use of which requires that a BAM index file (<filename>.bai) exists.
● Data Source:
BioConductor
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