population-genetics

There are 278 repositories under population-genetics topic.

  • anvio

    merenlab/anvio

    An analysis and visualization platform for 'omics data

    Language:Python447301.7k145
  • projectglow/glow

    An open-source toolkit for large-scale genomic analysis

    Language:Scala27220162109
  • knausb/vcfR

    Tools to work with variant call format files

    Language:R2501719254
  • lh3/psmc

    Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

    Language:C156196060
  • nf-core/eager

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Language:Nextflow15316143581
  • pophelper

    royfrancis/pophelper

    An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.

    Language:R144139038
  • SNPGenie

    chasewnelson/SNPGenie

    Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

    Language:Perl110107637
  • starskyzheng/panpop

    Application of pan-genome for population

    Language:Perl1002629
  • grenepipe

    moiexpositoalonsolab/grenepipe

    A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.

    Language:Python9545921
  • bacpop/PopPUNK

    PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

    Language:Python94622220
  • BGI-shenzhen/VCF2Dis

    VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Format

    Language:C++823420
  • poppr

    grunwaldlab/poppr

    🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

    Language:R681318026
  • AI-sandbox/neural-admixture

    Rapid population clustering with autoencoders

    Language:Python675199
  • precimed/mixer

    Causal Mixture Model for GWAS summary statistics

    Language:C67229618
  • lczech/genesis

    A library for working with phylogenetic and population genetic data.

    Language:C++589512
  • CBIIT/LDlinkR

    LDlinkR

    Language:R5683311
  • bodkan/slendr

    Population genetic simulations in R 🌍

    Language:R5591126
  • vinuesa/get_phylomarkers

    A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

    Language:Perl544178
  • kr-colab/diploSHIC

    feature-based deep learning for the identification of selective sweeps

    Language:Python5034214
  • kr-colab/locator

    deep learning prediction of geographic location from individual genome sequences

    Language:Python4651818
  • mklarqvist/tomahawk

    Fast calculations of linkage-disequilibrium in large-scale human cohorts

    Language:C++425169
  • Zilong-Li/PCAone

    Fast, Accurate and Memory-Efficient Principal Component Analysis All in One

    Language:C++42752
  • grenedalf

    lczech/grenedalf

    Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments

    Language:C++353363
  • gtonkinhill/rhierbaps

    rhierbaps: R implementation of hierBAPS

    Language:R345213
  • alek0991/iSAFE

    Pinpoints the mutation favored by selection

    Language:Python3341711
  • molpopgen/fwdpy11

    Forward-time simulation in Python using fwdpp

    Language:C++3034316
  • bodkan/admixr

    An R package for reproducible and automated ADMIXTOOLS analyses

    Language:R284779
  • EricArcher/strataG

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

    Language:HTML25106012
  • jgx65/hierfstat

    the hierfstat package

    Language:HTML2496813
  • Zilong-Li/vcfpp

    a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

    Language:C++23213
  • aprilweilab/grgl

    Genotype Representation Graph Library

    Language:C++22131
  • CBIIT/nci-webtools-dceg-linkage

    LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups. Each included application is specialized for querying and displaying unique aspects of linkage disequilibrium.

    Language:Python2217511
  • stephenturner/kgp

    1000 Genomes Project Metadata R Package

    Language:R19373
  • fengcong3/HAPPE

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

    Language:Python18270
  • sanjaynagi/rna-seq-pop

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

    Language:Jupyter Notebook182819
  • SchriderLab/Timesweeper

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

    Language:Python181692