radseq

There are 0 repository under radseq topic.

• thierrygosselin / radiator

  RADseq Data Exploration, Manipulation and Visualization using R

  radseqradseq-dataimputationgenotype-likelihoodsfiltergeneticsmissingnessoutliersgenomicsgenomic-data-analysisgenomics-visualizationgbsgenotyping-by-sequencingvisualizationoutliers-detectionheterozygosityparalogsartifacts-detectionbatch-effectsnormalization
  Language:HTML 57

• thierrygosselin / stackr

  stackr: an R package to run stacks software pipeline

  radseqradgenotype-likelihoodsfiltergeneticsgenomicsgenomic-data-analysisgenomics-visualizationradseq-datagbsgenotyping-by-sequencingstackr
  Language:R 27

• pimbongaerts / radseq

  Collection of Python scripts for parsing/analyses of RAD-seq data

  pythonradseqvcfpyradsnps
  Language:Python 20

• 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.

  population-assignmentpopulation-genomicsmachine-learningrradseqgbsdata-integrationcross-validation
  Language:R 17
• assigner

  thierrygosselin / assigner

  Population assignment analysis using R

  genomicsdatascienceassignment-analysisassignmentradseqradseq-datafstgbsgenotyping-by-sequencing
  Language:R 17

• tkchafin / scripts

  Random scripts, mostly for dealing with RADseq data and DNA sequence alignments

  radseqradseq-dataphylogeneticspopulation-genetics
  Language:Perl 15

• 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)

  radradseqgbsparalogipyrad
  Language:Python 10

• edgardomortiz / fineRADstructure-tools

  Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

  fineradstructurehaplotypesradseqgbsstructurepyradipyradstacks
  Language:Python 9
• grur

  thierrygosselin / grur

  grur: an R package tailored for RADseq data imputations

  genomicsgenomics-visualizationgenomic-data-analysisimputationradseqradseq-datagbsmachine-learningrandom-forestboosting-algorithmspca-analysismissing-data
  Language:R 7

• tkchafin / fragmatic

  Simple program for in silico restriction digest of genomic sequences, to simulate RAD-family NGS library prep methods

  ddrad-seqsilico-restriction-digestradseq
  Language:Perl 6

• pseudogene / radmap

  Analyse RAD-tags and generate the Genetic Map with GWAS

  bioinformaticsdockergwasradseqgenetic
  Language:Perl 5

• Grelot / seaConnect--dDocent

  GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

  gbsgenomicsvariant-callingradseqddocentstacksingularitysnakemakedemultiplexingsnpgenotypingsingularity-recipevcffastqpopulation-geneticsbioinformatics
  Language:Shell 2

• AlexFHart / RADSeq-Pipeline

  This repository contains a number of bash and R scripts used in the processing of RADSeq data on the VSC supercomputer.

  bioinformaticsradseq
  Language:Shell 1

• btmartin721 / ddrad_scripts

  Random scripts for dealing with ddRAD data, including output from pyRAD

  pyradddradradseqstatsiq-tree
  Language:Python 1

• cmdoret / CSD_Lfabarum

  Genomics pipeline to reproduce the analysis from Matthey-Doret et al., 2019, Genome Biology and Evolution

  genomicsdata-analysisbiologyevolutionradseqbioinformatics
  Language:Shell 1

• 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

  population-genomicsradseq-dataradseqpopulation-geneticsgenomic-data-analysisgenomics-visualizationgenomics-data
  1

• pimbongaerts / bermuda-rad

  Electronic notebook for "Deep reefs are not universal refuges: reseeding potential varies among coral species" (Science Advances, 2017)

  radseqcoralsymbiodiniumelectronic-notebookspython
  Language:Python 1

• thierrygosselin / genomics-workshops

  Populations genomics in R, Workshop in Hobart, Tasmania

  genomicsradseqdartseqworkshop
  1

• 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.

  radseqradseq-datapopulation-genomicspopulation-geneticsgenomics-visualizationgenomics
  0

• rancilhac / optiRADCT

  pipeline for optimizing the clustering threshold in ipyrad RADseq assemblies

  genomicsphylogeneticsradseq
  Language:Shell 0

• TimBoeh / Muscari_ddRAD

  Assembly, analysis and visualization of ddRAD seq data for the plant genus Muscari.

  jupyter-notebookphylogeneticsplantspythonradseq
  Language:Jupyter Notebook 0

• V-Z / RAD-Seq-scripts

  Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.

  bioinformaticsbioinformatics-analysisbioinformatics-pipelinebioinformatics-scriptsdata-analysisdata-sciencegenomicsmetacentrummolecular-biologyngsngs-analysisngs-pipelinepopulation-genomicsradseqradseq-data
  Language:Shell 0

• Grelot / reserveBenefit--snpsdata_analysis

  Codes i wrote for the paper "genomic resources for Mediterranean fishes"

  reservebenefitradseqgenomesnpbashrvcftoolsbedtoolssamtoolsbwa-mempython3bcftoolscontainersingularityhtslib
  Language:Shell