population-genomics

There are 10 repositories under population-genomics topic.

• knausb / vcfR

  Tools to work with variant call format files

  vcf-datarstatsgenomicsvisualizationrcpppopulation-geneticspopulation-genomics
  Language:R 235

• kr-colab / ReLERNN

  Recombination Landscape Estimation using Recurrent Neural Networks

  population-genomicsdeep-learningrecurrent-neural-networksrecombination
  Language:Python 44

• fgvieira / ngsLD

  Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

  ldgenotype-likelihoodspopulation-genomicsngs
  Language:C++ 37

• gtonkinhill / rhierbaps

  rhierbaps: R implementation of hierBAPS

  population-genomicspopulation-geneticspopulation-structurer
  Language:R 33

• kehrlab / PopDel

  Population-wide Deletion Calling

  bioinformaticsvariant-callingpopulation-genomicssv-callingstructural-variation
  Language:C++ 33

• ksiewert / BetaScan

  Genome-wide scan for balancing selection using beta statistic

  evolutionpopulation-genomicsbalancing-selectionnatural-selection
  Language:Python 25

• pievos101 / PopGenome

  An Efficient Swiss Army Knife for Population Genomic Analyses in R

  population-genomicssnpsgenome-analysis
  Language:R 25

• EricArcher / strataG

  strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.

  population-structurelocus-summariespopulation-geneticspopulation-genomicsgeneticssnpssnp-datadna-sequencesmicrosatellites
  Language:HTML 24

• mfumagalli / ImaGene

  Estimation of population genetic parameters using deep learning

  deep-learningneural-networkpopulation-genomics
  Language:Jupyter Notebook 24

• jgx65 / hierfstat

  the hierfstat package

  rhierfstatdevtoolspopulation-geneticspopulation-genomicskinshipquantitative-geneticsgwasfstatisticssimulationsr-packagerstats
  Language:HTML 23

• alexlancaster / pypop

  PyPop: Python for Population Genomics

  population-genomicsevolutionary-biologybioinformaticsopen-sourcefree-software
  Language:Python 19

• fgvieira / ngsF

  Estimation of per-individual inbreeding coefficients under a probabilistic framework

  population-genomicsinbreedingngsgenotype-likelihoods
  Language:C 18

• 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

• sanjaynagi / rna-seq-pop

  Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

  snakemake-workflowrna-seqvariant-callingdifferential-expressionpopulation-genomicssnakemaketranscriptomicsworkflowpopulation-geneticsselectionkaryotypeancestrygenomic-surveillance
  Language:Jupyter Notebook 17

• fengcong3 / HAPPE

  A tool to visualize the haplotype pattern and various information in excel.

  haplotypepopulation-geneticspopulation-genomicsread-depthtree
  Language:Python 16

• SchriderLab / Timesweeper

  Python package for detecting positive selective sweeps using time-series genomics sampling data.

  convolutional-neural-networksgeneticsneural-networkspopulation-geneticspopulation-genomics
  Language:Python 16

• fgvieira / ngsF-HMM

  Estimation of per-individual inbreeding tracts under a probabilistic framework

  population-genomicsinbreedingngsgenotype-likelihoodshmm
  Language:C++ 13

• xin-huang / dadi-cli

  Automated and distributed population genetic model inference from allele frequency spectra

  population-genomicsnatural-selectiondistribution-of-fitness-effectsdemographic-inference
  Language:Python 13

• sa-lee / starmie

  starmie: plotting and inference for population structure models :star2:

  population-genomicspopulation-geneticspopulation-structurerdata-visualization
  Language:R 12

• jbpease / mvftools

  Multisample Variant Format ToolKit

  molecular-evolutionpopulation-genomicspopulation-geneticsphylogeneticsphylogenomicsgenomics
  11

• wurmlab / genomicscourse

  For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics

  bioinformaticseducationgenome-analysisgenome-assemblypopulation-genomicspracticalsqmul
  Language:HTML 11

• fgvieira / ngsDist

  Estimation of pairwise distances under a probabilistic framework

  population-genomicsgenetic-distancesngsgenotype-likelihoods
  Language:C++ 10

• rtfcoimbra / Coimbra-et-al-2021_CurrBiol

  Code used to analyse WGS data of giraffe in Coimbra et al. 2021

  bioinformaticsgenomicsphylogenomicspopulation-genomicsspeciationgiraffe
  Language:Shell 10

• zhuochenbioinfo / PopGen

  Small scripts for population genetics analysis

  population-genomicspopulation-geneticsbioinformaticsgenomicsfasta-sequencevcfeigenstart-genotreemix
  Language:Perl 9

• albertopessia / Kpax3.jl

  Bayesian bi-clustering of categorical data

  bi-clusteringmcmc-samplerbayesian-cluster-analysisclusteringco-clusteringpopulation-genomicsgenomicscategorical-datamultivariate-datamultivariate-analysiscluster-analysis
  Language:Julia 8

• BiomedSciAI / Geno4SD

  An python omics data toolkit for the analysis across biological scales

  cancer-genomicsdnamachine-learningomicsomics-datapopulation-geneticspopulation-genomics
  Language:Jupyter Notebook 8

• Crazzy-Rabbit / Script-in-Bio

  生物信息学分析中用到的脚本

  bioinformaticscnv-analysispopulation-genomicsrna-seq-analysisngs-analysis
  Language:Jupyter Notebook 8

• V-Z / course-r-mol-data

  R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.

  rmolecular-biologymolecular-evolutioncourselearningscriptsscriptingdata-analysisdata-visualizationmolecular-databioconductorphylogeneticsphylogenetic-treesphylogenypopulation-geneticspopulation-genomicspopulation-structurebiogeographyphylogeographyevolution
  Language:TeX 8

• Zilong-Li / vcfppR

  vcfpp.h + htslib + Rcpp = fast VCF/BCF https://doi.org/10.1093/bioinformatics/btae049

  bioinformaticsfastrvcfhtslibpopulation-geneticspopulation-genomicsrstatsvcf-datavisulization
  Language:C 8

• jdalapicolla / LanGen_pipeline_version2

  Scripts in R for Landscape Genomics Analyses v.2

  genomicslandscapelandscape-genomicsphylogeographypipelinepopulation-genomicsvcfvcftools
  Language:R 7

• KiranJavkar / PRAWNS

  PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features

  population-genomicscomparative-genomicswhole-genome-genotypingpan-genome-analysisbioinformaticsgenomicscomputational-biologyantimicrobial-resistancebacterial-gwasantibiotic-resistancewhole-genome-sequencingwhole-genome-alignmentgenome-analysisparallel-programmingassociation-studiesmicrobial-genomics
  Language:C++ 7

• sunyatin / ASCEND

  Method to estimate the age and intensity of recent bottlenecks/founder events, using genotype data and a recombination map.

  allelesbottleneckdemographic-inferencedemographic-modelfounder-eventsidentity-by-descentpopulation-geneticspopulation-genomicsancient-dnademographic-history
  Language:Python 7

• xin-huang / sstar

  Detecting Archaic Introgression from Population Genetic Data with S*

  introgressionpopulation-genomicspython
  Language:Python 6

• janawold1 / PhD_thesis

  Presented here are the tools and strategies implemented for short-read SV discovery (Chapter 3), a population genomics study (Chapter 4) and genome graph construction (Chapter 5).

  biologypopulation-genomicsbirdsgraduate-project
  Language:Shell 5

• NBISweden / workshop-pgip

  Population Genomics in Practice main website

  population-genomics
  Language:TeX 5

• kfarleigh / PopGenHelpR

  PopGenHelpR is an R package that estimates commonly used population genomic statistics and generates publication quality figures.

  diversityfstheterozygosityinterpolationneispopulation-geneticspopulation-genomicsrsnmfstructurevcfprivate-alleles
  Language:R 3