Scripts and notes on how to analyse ancient DNA genotype data to understand population structure
☆49Jul 27, 2023Updated 3 years ago
Alternatives and similar repositories for ADMIXTURE-smartPCA-PLINK-and-EIGENSOFT
Users that are interested in ADMIXTURE-smartPCA-PLINK-and-EIGENSOFT are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert be…☆25Aug 9, 2023Updated 3 years ago
- Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.☆11Mar 27, 2020Updated 6 years ago
- An R script to generate plots for ADMIXTURE runs, for multiple K values.☆19Feb 27, 2025Updated last year
- This is a tool to estimate pairwise relatedness from ancient DNA, taking in account contamination, ROH, ascertainment bias.☆17Aug 6, 2024Updated 2 years ago
- Detecting IBD within low coverage ancient DNA data. Development Repository for software package that contains code for manuscript.☆17Sep 5, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆53May 12, 2026Updated 4 months ago
- analysis and plotting code for "Admixture into and within Africa" by George Busby et al 2016 (eLife)☆12Jun 16, 2016Updated 10 years ago
- ☆16Feb 11, 2022Updated 4 years ago
- A toolkit to calculate polygenic scores using PLINK2, PRS-CS, RapidoPGS, or PRSice2.☆16Aug 16, 2024Updated 2 years ago
- ☆18Dec 3, 2024Updated last year
- Program for estimating admixture proportions and doing principal component analysis of a single NGS sample☆12Sep 15, 2026Updated 3 weeks ago
- genome annotation (RNAseq and TE) pipeline (draft)☆13Sep 17, 2026Updated 3 weeks ago
- Scripts for analysis used during the course☆98Apr 30, 2024Updated 2 years ago
- A python script to calculate the relative coverage of X and Y chromosomes, and their associated error bars, from the depth of coverage at…☆16May 2, 2023Updated 3 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Experimental EIGENSOFT performance improvements.☆22Nov 1, 2014Updated 11 years ago
- A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage☆22Nov 18, 2023Updated 2 years ago
- A pipeline that accepts a VCF file to run through Admixture☆66May 3, 2026Updated 5 months ago
- Scripts to convert between file formats for various analyses☆16May 10, 2025Updated last year
- a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.☆27Jun 7, 2026Updated 4 months ago
- A course with Jupyter Notebooks for Computational Population Genetics☆10Sep 4, 2022Updated 4 years ago
- ☆13Aug 18, 2023Updated 3 years ago
- Notes on SNP-related tools and genome variation analysis☆29Sep 29, 2026Updated last week
- ☆21Nov 15, 2024Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Time-stratified f-statistics☆18Aug 1, 2025Updated last year
- Workflow for processing Illumina sequencing runs for ancient human DNA☆28Oct 29, 2020Updated 5 years ago
- ☆12Jun 12, 2023Updated 3 years ago
- This project is a collection of tools for bioinformatic processing of ancient DNA data at the Harvard Medical School Reich Lab.☆30Aug 21, 2026Updated last month
- issues for semina "Data Visulization"☆13Dec 23, 2025Updated 9 months ago
- Fast analysis and visualization of latent clusters in population genetic data☆77Mar 29, 2022Updated 4 years ago
- Here we present a method to plot the outputs of RFMIX version 2☆32Jul 1, 2026Updated 3 months ago
- tips and tricks in genome-wide association studies - a tutorial☆14Jul 25, 2023Updated 3 years ago
- Codes for Vmap1.1 and Vmap3☆11Jan 5, 2026Updated 9 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A complete Snakemake pipeline for detecting allele specific expression in RNA-seq☆10Jul 10, 2021Updated 5 years ago
- Suite of tools for pangenomics built using vg☆25Updated this week
- Python Scripts for Bioinformatics☆15Apr 24, 2024Updated 2 years ago
- Eigen tools by Nick Patterson and Alkes Price lab☆207Jul 20, 2026Updated 2 months ago
- BITE: BioInformatics tools for everyone☆22Jul 25, 2024Updated 2 years ago
- Fast, Accurate and Memory-Efficient Principal Component Analysis All in One For Large-scale Dataset☆55Updated this week
- Repository with documentation file of our Jan 22-24 workshop on Computational Population Genetics in Jena, Germany.☆15Aug 14, 2026Updated last month