Genomic Region Processing using Tools Such as 'BEDTools',
'BEDOPS' and 'Tabix'
Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'.
These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging.
bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
News
bedr 1.0.4
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Added rmarkdown in Suggests section
Parameterised test.region.similarity() with gaps.file and repeats.file to support custom files
Fixed bug when bedtools 'coverage' output is post-processed in bedr
Fixed is.valid.seq() to comply with inputs and outputs as described in docs
Exposed utility function bed2index() via NAMESPACE to support its direct usage
bedr 1.0.3
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Standardised function name; renamed snm() to bedr.snm.region()
Listed SystemRequirements to the package metadata
Added support for Human hg38 genome assembly
bedr 1.0.2
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Fixed compatibility with data.table >= v1.9.6 for data.table::fread() call
bedr 1.0.1
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Fixed sort --version command as Solaris does not support --version which is GNU specific