Set of utility functions for use with GenomicRanges
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Install R-4.0 or later
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Install devtools
install.packages('devtools')
install.packages('testthat')
- Install readsupport and dependent packages
## allows dependencies that throw warnings to install
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)
devtools::install_github('mskilab/readsupport')
What (short or long) reads support a given (known) rearrangement? This analysis is important for vetting or merging rearrangement calls, for genotyping new samples, and for co-calling.
readsupport allows you to assess the read support for a junction or arbitrary
rearranged contig (including those representing a multi-part rearrangements).
It is built on top of gGnome, RSeqLib, and GenomicRanges.
Examples under construction!
Marcin Imielinski - Associate Professor, Weill Cornell Medicine; Core Member, New York Genome Center
Zi-Ning Choo - MD-PhD student, Tri-Institutional MD PhD program, Cornell University
Alon Shaiber - Genomics Data Scientist, Imielinski Lab, Weill Cornell Medicine