readsupport

Set of utility functions for use with GenomicRanges

Installation

1. Install R-4.0 or later

2. Install devtools

install.packages('devtools')
install.packages('testthat')

3. 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')

Read Support

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!

Attributions

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