Map intervals on one genome to search spaces on another genome using
a synteny map
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).
This work is funded by the National Science Foundation grant:
NSF-IOS 1546858 Orphan Genes: An Untapped Genetic Reservoir of Novel Traits
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).
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.
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