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Changelog

Source: NEWS.md

footprintR 0.2.0

  • Harmonization of function and argument names (using camelCase)
  • Use BiocParallel::BPPARAM in functions that support parallel execution
  • Rename addReadsSummary() to flattenReadLevelAssay()

footprintR 0.1.4

  • Refactored plotRegion() to use a single tracks argument instead of tracks.summary and tracks.reads.
  • Allow filterReads() to return the filter statistics table without subsetting the SummarizedExperiment object.
  • Add readModBam(..., variantPositions) argument that adds labels to reads, enabling allele specific analyses.

footprintR 0.1.3

  • Added option to decompress bam records in readModBam() in parallel on multiple threads.

footprintR 0.1.2

  • Added a NEWS.md file to track changes to the package.
  • Use SparseArray::NaArray assays to represent read-level modification probabilities.