radseq
There are 23 repositories under radseq topic.
thierrygosselin/radiator
RADseq Data Exploration, Manipulation and Visualization using R
thierrygosselin/stackr
stackr: an R package to run stacks software pipeline
pimbongaerts/radseq
Collection of Python scripts for parsing/analyses of RAD-seq data
alexkychen/assignPOP
Population Assignment using Genetic, Non-genetic or Integrated Data in a Machine-learning Framework. Methods in Ecology and Evolution. 2018;9:439–446.
thierrygosselin/assigner
Population assignment analysis using R
tkchafin/scripts
Random scripts, mostly for dealing with RADseq data and DNA sequence alignments
edgardomortiz/paralog-finder
Detects and blacklists paralog RAD loci analyzed in Stacks or ipyrad, based on the McKinney 2017 method (doi:10.1111/1755-0998.12613)
edgardomortiz/fineRADstructure-tools
Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)
thierrygosselin/grur
grur: an R package tailored for RADseq data imputations
tkchafin/fragmatic
Simple program for in silico restriction digest of genomic sequences, to simulate RAD-family NGS library prep methods
pseudogene/radmap
Analyse RAD-tags and generate the Genetic Map with GWAS
Grelot/seaConnect--dDocent
GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.
AlexFHart/RADSeq-Pipeline
This repository contains a number of bash and R scripts used in the processing of RADSeq data on the VSC supercomputer.
btmartin721/ddrad_scripts
Random scripts for dealing with ddRAD data, including output from pyRAD
cmdoret/CSD_Lfabarum
Genomics pipeline to reproduce the analysis from Matthey-Doret et al., 2019, Genome Biology and Evolution
LauricReynes/FIS_distribution
R script employed in the manuscript 'Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii' to compute the distribution of FIS across loci into discrete classes
pimbongaerts/bermuda-rad
Electronic notebook for "Deep reefs are not universal refuges: reseeding potential varies among coral species" (Science Advances, 2017)
rancilhac/optiRADCT
pipeline for optimizing the clustering threshold in ipyrad RADseq assemblies
thierrygosselin/genomics-workshops
Populations genomics in R, Workshop in Hobart, Tasmania
LauricReynes/Clonal_assessment
R script employed in the manuscript 'Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii' to compute the frequency of pairwise genetic distances among individuals.
TimBoeh/Muscari_ddRAD
Assembly, analysis and visualization of ddRAD seq data for the plant genus Muscari.
V-Z/RAD-Seq-scripts
Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.
Grelot/reserveBenefit--snpsdata_analysis
Codes i wrote for the paper "genomic resources for Mediterranean fishes"