population-genomics

Tools to work with variant call format files

Recombination Landscape Estimation using Recurrent Neural Networks

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

An Efficient Swiss Army Knife for Population Genomic Analyses in R

rhierbaps: R implementation of hierBAPS

Population-wide Deletion Calling

Genome-wide scan for balancing selection using beta statistic

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.

the hierfstat package

Estimation of population genetic parameters using deep learning

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

Some script and skills in Population Genetic analyzes

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

PyPop: Python for Population Genomics

Upscaling SV detection to a multi-population level.

Estimation of per-individual inbreeding coefficients under a probabilistic framework

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

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

Automated and Distributed Population Genetic Model Inference from Allele Frequency Spectra

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