plyranges is a dplyr like API to the Ranges/GenomicRanges infrastructure in Bioconductor.
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")
Useful links:
Report bugs at https://github.com/sa-lee/plyranges