`GenomicRanges` cheat sheet
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@chiragparsania-13271
Last seen 8 days ago
Australia

Every time I want to use ranges-related functions from the package GenomicRanges I need to explore docs again and again. Is this common to everyone? What's the best way to remember what GRanges functions (e.g. shift, reduce, join, disjoin, intersect, etc.) do? Like does anyone know if there's any pictorial representation or cheat sheet to remember GRanges functions? I have found one (attached here) in the package documentation. Any better than this?

enter image description here

GenomicRanges • 166 views
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@mikelove
Last seen 1 hour ago
United States

Not pictoral, but I wrote up this table a while ago for quick reference:

https://github.com/mikelove/bioc-refcard/blob/master/README.Rmd#L149

I often now use and teach plyranges, as students are familiar with dplyr and the language adapts easily, including grouping and summarization.

https://sa-lee.github.io/plyranges/articles/an-introduction.html#arithmetic-on-ranges-1

shift(x, 5) is: shift_right(x, 5) or _upstream and _downstream can be used to move with respect to strand. The vignette above has more examples. Anchoring various points in the range and mutating the width is easy to write and read in my opinion.

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Thanks, Love. Good to know about plyranges. I will play with that.

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