Synder

Map intervals on one genome to search spaces on another genome using
a synteny map

Citation

If you use this tool, please cite:

Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, and Eve Wurtele. "synder: inferring genomic orthologs from synteny maps." BioRxiv (2019).

Funding

This work is funded by the National Science Foundation grant:

NSF-IOS 1546858 Orphan Genes: An Untapped Genetic Reservoir of Novel Traits

Installation

In an R session

library(devtools)
install_github('arendsee/synder')

To build the vignettes in an R shell run

library(devtools)
devtools::build_vignettes()

If you use RStudio, then there is probably some button for this (GUIs are too volatile for me to say anything terribly helpful).

Troubleshooting

If you get an error during install saying:

** preparing package for lazy loading                                                              
Error : object 'extract' not found whilst loading namespace 'R.utils'
ERROR: lazy loading failed for package ‘synder’                                
* removing ‘/home/<username>/R/x86_64-pc-linux-gnu-library/3.4/synder’           
Error: Command failed (1) 

Try removing the packages R.oo and R.utils and then, in a vanilla setting without magrittr loaded, reinstall them. Then try installing synder.

If you get weird errors in the data, for example data(toy) and then see a lot of hash marks in the GFF files. Then start a new session, load GenomicRanges and Biostrings. Then try reloading synder.

Documentation

First read the "intro" vignette

library(synder)
vignette("intro", package="synder")

Other vignettes can be listed with vignette(package="synder").

Information on specific command is available through normal channels:

library(synder)
?synder::search
?synder::anon_search