meeranhussain/Population_genomic_analysis

A repository for efficient population genomic analysis using Snakemake workflow.

Language: R - Size: 919 KB - Last synced at: about 1 hour ago - Pushed at: about 3 hours ago - Stars: 0 - Forks: 0

xin-huang/sai

Statistics for Adaptive Introgression

Language: Python - Size: 6.34 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 2

kehrlab/PopDel

Population-wide Deletion Calling

Language: C++ - Size: 20.5 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 35 - Forks: 2

zjnolen/PopGLen

Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.

Language: Python - Size: 18.6 MB - Last synced at: 3 days ago - Pushed at: 12 days ago - Stars: 10 - Forks: 1

TeddYenn/population_genomics-edamame

Population Genomics: For Selection Footprints in Edamame

Language: TeX - Size: 2.32 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

xin-huang/dadi-cli

Automated and distributed population genetic model inference from allele frequency spectra

Language: Python - Size: 119 MB - Last synced at: 1 day ago - Pushed at: 15 days ago - Stars: 16 - Forks: 7

Zilong-Li/vcfppR

The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049

Language: C - Size: 13.6 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 15 - Forks: 3

alexlancaster/pypop

PyPop: Python for Population Genomics

Language: Python - Size: 67.2 MB - Last synced at: 7 days ago - Pushed at: 13 days ago - Stars: 25 - Forks: 14

kr-colab/ReLERNN

Recombination Landscape Estimation using Recurrent Neural Networks

Language: Python - Size: 1.02 MB - Last synced at: 7 days ago - Pushed at: 19 days ago - Stars: 58 - Forks: 11

sanjaynagi/rna-seq-pop

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

Language: Jupyter Notebook - Size: 99.5 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 18 - Forks: 9

mfumagalli/ImaGene

Estimation of population genetic parameters using deep learning

Language: Jupyter Notebook - Size: 148 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 28 - Forks: 10

EricArcher/strataG

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

Language: HTML - Size: 26.7 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 25 - Forks: 12

xin-huang/sstar

Detecting Archaic Introgression from Population Genetic Data with S*

Language: Python - Size: 64.5 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 6 - Forks: 4

fgvieira/ngsF-HMM

Estimation of per-individual inbreeding tracts under a probabilistic framework

Language: C++ - Size: 303 KB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 6

knausb/vcfR

Tools to work with variant call format files

Language: R - Size: 20.9 MB - Last synced at: 18 days ago - Pushed at: about 2 months ago - Stars: 257 - Forks: 53

molpopgen/demes-rs

rust tools for the demes ecosystem

Language: Rust - Size: 680 KB - Last synced at: 19 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 1

jgx65/hierfstat

the hierfstat package

Language: HTML - Size: 1010 KB - Last synced at: 2 days ago - Pushed at: 5 months ago - Stars: 24 - Forks: 13

AstraBert/drosmel-in-asia

Drosophila melanogaster IndSeq and PoolSeq genomics data in Asia and Europe

Language: HTML - Size: 6.51 MB - Last synced at: 9 days ago - Pushed at: 27 days ago - Stars: 1 - Forks: 0

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.

Language: R - Size: 8.81 MB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 16 - Forks: 4

fengcong3/HAPPE

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

Language: Python - Size: 12.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 18 - Forks: 0

huiqingyeooo/Ae_albopictus_popgen

Codes for analyzing Aedes albopictus ddRADSeq data

Language: R - Size: 21.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

natforsdick/kuaka-population-genomics

Population genomics for Kuaka Whenua Hou | Whenua Hou diving petrels and Kuaka | Common diving petrels

Language: Shell - Size: 91.8 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

SchriderLab/Timesweeper

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

Language: Python - Size: 5.17 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 2

IgnasiLucas/hedgehog_RAD Fork of eliasok/hedgehog_RAD

Hedgehog genomic project using RAD paired-end reads

Language: R - Size: 68.4 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

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.

Language: TeX - Size: 1.46 GB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 4

NBISweden/workshop-pgip-H23

Population Genomics in Practice main website

Language: TeX - Size: 234 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 3

janawold1/2024_MolEcol_ConsGen_Special_Issue

A repository containing code for a manuscript intended for Molecular Ecology.

Language: Jupyter Notebook - Size: 29.1 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

hernanmd/REHH2-docker

Dockerfile for REHH version 2.0.4

Language: R - Size: 46.9 KB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

V-Z/structure-sum

Script to summarize the results from several structure runs

Language: R - Size: 28.3 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

fgvieira/ngsLD

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

Language: C++ - Size: 301 KB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 46 - Forks: 8

BiomedSciAI/Geno4SD

An python omics data toolkit for the analysis across biological scales

Language: Jupyter Notebook - Size: 78.1 MB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 1

Karim-Mane/mpbr

Population Genomics Analysis for Plasmodium falciparum

Language: R - Size: 84.9 MB - Last synced at: 9 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

xin-huang/gaia

Genomic Analysis of Introgressed Alleles with Machine Learning

Language: Python - Size: 2.65 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 1

wurmlab/genomicscourse

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

Language: HTML - Size: 1.31 GB - Last synced at: 11 days ago - Pushed at: 7 months ago - Stars: 12 - Forks: 20

gtonkinhill/rhierbaps

rhierbaps: R implementation of hierBAPS

Language: R - Size: 1.63 MB - Last synced at: 5 days ago - Pushed at: almost 4 years ago - Stars: 34 - Forks: 3

fgvieira/ngsF

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Language: C - Size: 92.8 KB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 20 - Forks: 8

vis7219/PopGenAnalysis

This repository contains the pipeline script for Population Genetics Analysis built using SnakeMake

Language: Python - Size: 84.1 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

vlkofly/popgenome-metacentrum

Language: Shell - Size: 43 KB - Last synced at: 9 months ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 0

kfarleigh/PopGenHelpR

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

Language: R - Size: 14.6 MB - Last synced at: 17 days ago - Pushed at: 9 months ago - Stars: 3 - Forks: 0

remytuyeras/HaploDynamics

A python library to develop genomic data simulators

Language: Python - Size: 1.01 MB - Last synced at: 27 days ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

bredeson/Dioscorea-alata-genomics

Code and data from the Bredeson, Lyons, et al. Dioscorea alata var. TDa95/00328 v2 genome and analysis manuscript.

Language: R - Size: 207 MB - Last synced at: 6 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

sfbizzari/gnomADv4-Batch-tool-pythonAPI Fork of broadinstitute/gnomad-browser

Using gnomad-browser's GraphQL updated API to retrieve total joint allele frequencies, exome/genome allele frequencies and homozygote counts as well as population specific numbers for a batch of variants.

Language: Python - Size: 38.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

Crazzy-Rabbit/Script-in-Bio

生物信息学分析中用到的脚本

Language: Jupyter Notebook - Size: 9.86 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 8 - Forks: 5

pievos101/PopGenome

An Efficient Swiss Army Knife for Population Genomic Analyses in R

Language: R - Size: 923 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 25 - Forks: 3

etkayapar/bamRefine

Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog

Language: Python - Size: 4.72 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

LauricReynes/Temporal-genomics

A tutorial for reproducting outlier tests based on temporal differentiation

Size: 10.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

fgvieira/ngsDist

Estimation of pairwise distances under a probabilistic framework

Language: C++ - Size: 1.44 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 7

littleblackfish/rice3k

Workflow for calling variants using data from 3000 Rice Genomes project

Language: Shell - Size: 9.77 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 1

littleblackfish/heteroMutationRate

workflow for reproducing results of a nature paper

Language: Jupyter Notebook - Size: 600 KB - Last synced at: about 1 year ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

selotape/G-PhoCS Fork of gphocs-dev/G-PhoCS

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.

Language: C++ - Size: 3 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

janawold1/2023_MER_Special_Issue

Scripts supporting the manuscript submitted to the Molecular Ecology Resources Special Issue 'Omics for species conservation'

Language: Shell - Size: 91.8 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

ksiewert/BetaScan

Genome-wide scan for balancing selection using beta statistic

Language: Python - Size: 1.48 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 20 - Forks: 5

raveancic/aDNAYchromosome

Language: R - Size: 36.5 MB - Last synced at: 4 months ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

sa-lee/starmie 📦

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

Language: R - Size: 6.3 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 11 - Forks: 6

btmartin721/makePopMap

Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files

Language: Python - Size: 50.8 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1

jdalapicolla/LanGen_pipeline_version2

Scripts in R for Landscape Genomics Analyses v.2

Language: R - Size: 130 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 5

jdalapicolla/IBD_models.R

Scripts in R for analyses of Isolation by Distance (IBD) - PART 2 in LANDSCAPE GENOMICS PIPELINE

Language: R - Size: 69.3 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

santiagosnchez/poly-div_sfs

Estimates polymorphism and divergence parameters from FASTA alignments

Language: Perl - Size: 380 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 1

rtfcoimbra/Coimbra-et-al-2023_BMCBiol

Code used to analyse WGS data of giraffe in Coimbra et al. 2023

Language: R - Size: 81.1 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

rtfcoimbra/Coimbra-et-al-2021_CurrBiol

Code used to analyse WGS data of giraffe in Coimbra et al. 2021 (https://doi.org/10.1016/j.cub.2021.04.033)

Language: Shell - Size: 83 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 6

jbpease/mvftools

Multisample Variant Format ToolKit

Size: 4.18 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 11 - Forks: 5

ECRRM/genomics-commons

Genomics Commons

Language: Jupyter Notebook - Size: 2.75 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

V-Z/structure-multi-pbspro

Set of scripts to run STRUCTURE in parallel on computing grids like MetaCentrum. Scripts are designed for grids and clusters using PBS Pro, but can be easily adopted for another queue system.

Language: Shell - Size: 83 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

zhuochenbioinfo/PopGen

Small scripts for population genetics analysis

Language: Perl - Size: 51.8 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 4

kfarleigh/ResearchersGuideToPopulationGenomics

A book that discusses topics and contains tutorials relevant to population genomics

Language: HTML - Size: 1.29 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

endreth/jVCFparser

A command-line parser for VCF files designed for population genetics analyses.

Language: Java - Size: 2.34 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

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).

Language: Shell - Size: 249 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 2

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

Language: C++ - Size: 6.7 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

jdalapicolla/MLPE.R

Scripts in R for analyses of Isolation by Resistance (IBR) - PART 3 in LANDSCAPE GENOMICS PIPELINE

Language: R - Size: 113 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 2

xin-huang/SeleDiff 📦

A fast and scalable tool for estimating and testing selection differences between populations

Language: Java - Size: 141 MB - Last synced at: 7 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

g-pacheco/PigeonBreedsGenomics

🕊 This repository is associated with the manuscript Pacheco et al. (2020).

Language: R - Size: 41.7 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

sunyatin/ASCEND

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

Language: Python - Size: 60 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 0

xin-huang/PopGenTools

A collection for available tools in population genetics

Size: 11.7 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0

AntoineHo/runGATK

Small GATK alignment and variant calling pipeline using python

Language: Python - Size: 91.8 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

V-Z/RAD-Seq-scripts

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

Language: Shell - Size: 5.14 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

albertopessia/Kpax3.jl

Bayesian bi-clustering of categorical data

Language: Julia - Size: 530 KB - Last synced at: 3 months ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 7

IgnasiLucas/fish

Language: R - Size: 3.4 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

nnbuainain/plot_ancest_coef_maps

A script to plot ancestral coefficients from population genetic analyses on maps

Language: R - Size: 33.5 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

M-Osky/population_genetics

Various unix and perl scripts to deal with genetics data: prepare submission files, extract results, and so. Check their "help" to see usage

Language: Perl - Size: 88.9 KB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

ChevronOne/Tools-For-Computational-Biology

Tools For Computational Biology

Language: C++ - Size: 2.81 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 1

crustaceana/TheFucusProject

All scripts to process and analyse genomic data, as well as, to calculate estimates of population genomics related to the brown seaweed from the Fucus genus.

Language: R - Size: 58.6 KB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

btmartin721/phylip2eigenstrat

Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile

Language: Python - Size: 238 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 1

mathemage/schrodinger-poster-2020

Poster for the Schrodinger Scholarship event 2020

Language: TeX - Size: 1.73 MB - Last synced at: 2 months ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

armanbilge/APG

ancient population genomics

Language: Scala - Size: 180 KB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

gentlewasp/ipm_popgenetics

Language: R - Size: 71.3 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 1

andrewkern/segSiteHMM

software implementation of the hidden Markov model developed in Kern and Haussler (2010)

Language: C - Size: 30.5 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

IgnasiLucas/mosquito

Language: Python - Size: 4.05 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 2

Mass23/Master

Language: Python - Size: 127 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

yvanlebras/STRAF Fork of agouy/straf

STR Analysis for Forensics

Language: R - Size: 867 KB - Last synced at: 10 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

tiagoantao/LD-chart

A Javascript chart for Linkage Disequilibrium (based on three.js)

Language: JavaScript - Size: 17.6 KB - Last synced at: about 1 month ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

yvanlebras/skeleSim Fork of christianparobek/skeleSim

Null models, performance testing, and power estimation with population simulations

Language: HTML - Size: 11.6 MB - Last synced at: 10 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

yvanlebras/MINOTAUR Fork of NESCent/MINOTAUR

Multivariate vIsualisatioN and OuTlier Analysis Using R

Language: R - Size: 77.5 MB - Last synced at: 10 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

TransGirlCodes/PhD_Thesis

The LaTeX source for my PhD Thesis, the viva for which took place in September, 2016.

Language: TeX - Size: 10.9 MB - Last synced at: 15 days ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0