genepopedit protocols

View genepopedit computational protocol

genepopedit statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Population structure inference chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

genepopedit specifications

Information


Unique identifier OMICS_20127
Name genepopedit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0.6
Stability Stable
Requirements
dplyr, data.table, reshape2, stringr
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Brendan Wringe <>
  • person_outline Ryan Stanley <>
  • person_outline Ian Bradbury <>
  • person_outline Nick Jeffery <>

Publication for genepopedit

genepopedit in pipeline

2017
PMCID: 5395438
PMID: 28428843
DOI: 10.1002/ece3.2872

[…] per rad tag was retained to remove the effects of physical linkage. the resulting panel was converted for subsequent analyses using pgdspider v2.0.8.3 (lischer & excoffier, ) and the r package genepopedit (stanley, jeffery, wringe, dibacco, & bradbury, 2017)., multiple approaches were used to identify loci putatively experiencing adaptive selection (outliers). we first employed […]


To access a full list of citations, you will need to upgrade to our premium service.

genepopedit in publications

 (3)
PMCID: 5717698
PMID: 29291123
DOI: 10.1098/rsos.171394

[…] snps missing data in greater than 15% of individuals and removed these. we filtered the north american and european datasets to 1773 loci common to all locations and snp arrays using the r package genepopedit []. while we note that our european data are unbalanced due to the inclusion of a high density of northern english and scottish rivers, we investigated whether random subsetting […]

PMCID: 5775496
PMID: 29387152
DOI: 10.1111/eva.12524

[…] set to default., we further reduced our panel for downstream feature selection by removing redundant snps and snps in linkage disequilibrium using the genepop_toploci function in the r package genepopedit (stanley, jeffery, wringe, dibacco, & bradbury, ) at an r 2 threshold of 0.2 and a minimum global f st of 0.05. although this is a highly stringent approach, reductions in the data […]

PMCID: 5395438
PMID: 28428843
DOI: 10.1002/ece3.2872

[…] per rad tag was retained to remove the effects of physical linkage. the resulting panel was converted for subsequent analyses using pgdspider v2.0.8.3 (lischer & excoffier, ) and the r package genepopedit (stanley, jeffery, wringe, dibacco, & bradbury, 2017)., multiple approaches were used to identify loci putatively experiencing adaptive selection (outliers). we first employed […]


To access a full list of publications, you will need to upgrade to our premium service.

genepopedit institution(s)
Bedford Institute of Oceanography, Dartmouth, NS, Canada; Department of Computer Science, Dalhousie University, Halifax, NS, Canada; Northwest Atlantic Fisheries Science Centre, St. John’s, NL, Canada
genepopedit funding source(s)
Funding for this work has been provided through the NSERC Canadian Healthy Oceans Network (CHONe) and the Genomics Research and Development Initiative of Fisheries and Oceans Canada.

genepopedit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review genepopedit