plyranges: a grammar of genomic data manipulation

plyranges is a dplyr like API to the Ranges/GenomicRanges infrastructure in Bioconductor.

Details

plryanges provides a consistent interface for importing and wrangling genomics data from a variety of sources. The package defines a grammar of genomic data manipulation through a set of verbs. These verbs can be used to construct human readable analysis pipelines based on Ranges objects.

• Modify genomic regions with the set_width() and stretch() functions.

• Modify genomic regions while fixing the start/end/center coordinates with the anchors() family of functions.

• Sort genomic ranges with arrange().

• Modify, subset, and aggregate genomic data with the mutate(), filter(), and summarise()functions.

• Any of the above operations can be performed on partitions of the data with group_by().

• Find nearest neighbour genomic regions with the join_nearest() family of functions.

• Find overlaps between ranges with the join_overlap_inner() family of functions.

• Merge all overlapping and adjacent genomic regions with reduce_ranges().

• Merge the end points of all genomic regions with disjoin_ranges().

• Import and write common genomic data formats with the read_/write_ family of functions.

For more details on the features of plryanges, read the vignette: browseVignettes(package = "plyranges")

See also

Useful links:

• https://tidyomics.github.io/plyranges

• Report bugs at https://github.com/tidyomics/plyranges

Author

Maintainer: Michael Love michaelisaiahlove@gmail.com [contributor]

Authors:

• Stuart Lee (ORCID)

• Michael Lawrence [contributor]

• Dianne Cook [contributor]

Other contributors:

• Spencer Nystrom (ORCID) [contributor]

• Pierre-Paul Axisa [contributor]