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: about 2 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

Zilong-Li/vcfppR

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

Language: C - Size: 12.4 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 8 - Forks: 1

kfarleigh/PopGenHelpR

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

Language: R - Size: 13.6 MB - Last synced: about 8 hours ago - Pushed: 2 days ago - Stars: 3 - 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: 3 days ago - Pushed: 4 days ago - Stars: 8 - Forks: 5

molpopgen/demes-rs

rust tools for the demes ecosystem

Language: Rust - Size: 602 KB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 1

xin-huang/dadi-cli

Automated and distributed population genetic model inference from allele frequency spectra

Language: Python - Size: 94 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 13 - Forks: 7

kr-colab/ReLERNN

Recombination Landscape Estimation using Recurrent Neural Networks

Language: Python - Size: 1.01 MB - Last synced: about 4 hours ago - Pushed: about 2 months ago - Stars: 44 - Forks: 11

alexlancaster/pypop

PyPop: Python for Population Genomics

Language: Python - Size: 57.1 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 19 - Forks: 16

SchriderLab/Timesweeper

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

Language: Python - Size: 5.17 MB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 16 - Forks: 2

sanjaynagi/rna-seq-pop

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

Language: Jupyter Notebook - Size: 99.6 MB - Last synced: 11 days ago - Pushed: 16 days ago - Stars: 17 - Forks: 6

pievos101/PopGenome

An Efficient Swiss Army Knife for Population Genomic Analyses in R

Language: R - Size: 900 KB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 25 - Forks: 3

knausb/vcfR

Tools to work with variant call format files

Language: R - Size: 21 MB - Last synced: 23 days ago - Pushed: 5 months ago - Stars: 233 - Forks: 55

LauricReynes/Temporal-genomics

A tutorial for reproducting outlier tests based on temporal differentiation

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

jgx65/hierfstat

the hierfstat package

Language: HTML - Size: 1000 KB - Last synced: 6 days ago - Pushed: about 1 year ago - Stars: 23 - Forks: 14

zjnolen/angsd-snakemake-pipeline

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

Language: Python - Size: 13.8 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 2 - Forks: 0

littleblackfish/rice3k

Workflow for calling variants using data from 3000 Rice Genomes project

Language: Shell - Size: 9.77 KB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 1

littleblackfish/heteroMutationRate

workflow for reproducing results of a nature paper

Language: Jupyter Notebook - Size: 600 KB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

mfumagalli/ImaGene

Estimation of population genetic parameters using deep learning

Language: Jupyter Notebook - Size: 137 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 24 - Forks: 10

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: about 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

natforsdick/kuaka-population-genomics

Population genomics for Kuaka Whenua Hou (Pelecanoides whenuahouensis) and Common diving petrels (Pelecanoides urinatrix)

Language: Shell - Size: 37.1 KB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 0 - Forks: 0

NBISweden/workshop-pgip

Population Genomics in Practice main website

Language: TeX - Size: 234 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 4 - Forks: 3

remytuyeras/HaploDynamics

A python library to develop genomic data simulators

Language: Python - Size: 1.01 MB - Last synced: 5 days ago - Pushed: 9 months ago - Stars: 2 - Forks: 0

xin-huang/sstar

Detecting Archaic Introgression from Population Genetic Data with S*

Language: Python - Size: 64.2 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 6 - Forks: 3

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: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0

BiomedSciAI/Geno4SD

An python omics data toolkit for the analysis across biological scales

Language: Jupyter Notebook - Size: 78.1 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 6 - Forks: 1

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: 5 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

ksiewert/BetaScan

Genome-wide scan for balancing selection using beta statistic

Language: Python - Size: 1.48 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 20 - Forks: 5

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: 3 months ago - Pushed: 3 months ago - Stars: 8 - Forks: 3

fgvieira/ngsLD

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

Language: C++ - Size: 301 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 33 - Forks: 7

gtonkinhill/rhierbaps

rhierbaps: R implementation of hierBAPS

Language: R - Size: 1.63 MB - Last synced: 6 months ago - Pushed: about 3 years ago - Stars: 30 - Forks: 3

fgvieira/ngsF

Estimation of per-individual inbreeding coefficients under a probabilistic framework

Language: C - Size: 92.8 KB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 18 - Forks: 8

xin-huang/SeleDiff 📦

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

Language: Java - Size: 141 MB - Last synced: 7 months ago - Pushed: over 2 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: 7 months ago - Pushed: over 5 years ago - Stars: 11 - Forks: 6

fgvieira/ngsF-HMM

Estimation of per-individual inbreeding tracts under a probabilistic framework

Language: C++ - Size: 303 KB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 13 - Forks: 6

fgvieira/ngsDist

Estimation of pairwise distances under a probabilistic framework

Language: C++ - Size: 1.44 MB - Last synced: 7 months ago - Pushed: 9 months ago - Stars: 9 - Forks: 6

EricArcher/strataG

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

Language: HTML - Size: 25.1 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 25 - Forks: 10

btmartin721/makePopMap

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

Language: Python - Size: 50.8 KB - Last synced: 7 months ago - Pushed: over 3 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: 7 months ago - Pushed: about 1 year 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: 7 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 1

santiagosnchez/poly-div_sfs

Estimates polymorphism and divergence parameters from FASTA alignments

Language: Perl - Size: 380 KB - Last synced: 7 months ago - Pushed: almost 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: 7 months ago - Pushed: 7 months 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: 7 months ago - Pushed: 7 months ago - Stars: 9 - Forks: 6

jbpease/mvftools

Multisample Variant Format ToolKit

Size: 4.18 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 11 - Forks: 5

ECRRM/genomics-commons

Genomics Commons

Language: Jupyter Notebook - Size: 2.75 MB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

fengcong3/HAPPE

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

Language: Python - Size: 12.3 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 13 - Forks: 0

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: 24 days ago - Pushed: 24 days ago - Stars: 11 - Forks: 19

kehrlab/PopDel

Population-wide Deletion Calling

Language: C++ - Size: 20.4 MB - Last synced: 22 days ago - Pushed: 23 days ago - Stars: 33 - Forks: 2

V-Z/structure-sum

Script to summarize the results from several structure runs

Language: R - Size: 27.3 KB - Last synced: 11 months ago - Pushed: 11 months 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: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 1

zhuochenbioinfo/PopGen

Small scripts for population genetics analysis

Language: Perl - Size: 51.8 KB - Last synced: 7 months ago - Pushed: 12 months ago - Stars: 7 - Forks: 4

vis7219/PopGenAnalysis

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

Language: Python - Size: 84.1 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

kfarleigh/ResearchersGuideToPopulationGenomics

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

Language: HTML - Size: 1.29 MB - Last synced: 25 days ago - Pushed: 25 days 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: 12 months ago - Pushed: about 1 year 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: 4 months ago - Pushed: about 1 year 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: about 1 year ago - Pushed: over 1 year 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: 3 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 2

g-pacheco/PigeonBreedsGenomics

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

Language: R - Size: 41.7 MB - Last synced: about 1 year ago - Pushed: almost 2 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: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - 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: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

xin-huang/PopGenTools

A collection for available tools in population genetics

Size: 11.7 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 2 - 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: about 2 months ago - Pushed: about 2 months ago - Stars: 17 - Forks: 4

AntoineHo/runGATK

Small GATK alignment and variant calling pipeline using python

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

albertopessia/Kpax3.jl

Bayesian bi-clustering of categorical data

Language: Julia - Size: 530 KB - Last synced: 3 days ago - Pushed: about 2 years ago - Stars: 8 - Forks: 7

IgnasiLucas/fish

Language: R - Size: 3.4 MB - Last synced: about 1 year ago - Pushed: about 2 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: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

ChevronOne/Tools-For-Computational-Biology

Tools For Computational Biology

Language: C++ - Size: 2.81 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 1 - Forks: 1

raveancic/aDNAYchromosome

Language: R - Size: 36.5 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

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: 4 months ago - Pushed: almost 4 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: 7 months ago - Pushed: about 6 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: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

armanbilge/APG

ancient population genomics

Language: Scala - Size: 180 KB - Last synced: 10 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

hernanmd/REHH2-docker

Dockerfile for REHH version 2.0.4

Language: R - Size: 46.9 KB - Last synced: 11 days ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

gentlewasp/ipm_popgenetics

Language: R - Size: 71.3 KB - Last synced: about 1 year ago - Pushed: about 5 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: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

IgnasiLucas/mosquito

Language: Python - Size: 4.05 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 2

Mass23/Master

Language: Python - Size: 127 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

yvanlebras/STRAF Fork of agouy/straf

STR Analysis for Forensics

Language: R - Size: 867 KB - Last synced: 29 days ago - Pushed: over 6 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: 27 days ago - Pushed: about 6 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: 29 days ago - Pushed: over 6 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: 29 days ago - Pushed: over 6 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: 25 days ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

IgnasiLucas/hedgehog_RAD Fork of eliasok/hedgehog_RAD

Hedgehog genomic project using RAD paired-end reads

Language: Python - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0