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General tools for genomic analyses.

Python 356 95 Updated Jul 23, 2024

Example 📓 Jupyter notebooks that demonstrate how to build, train, and deploy machine learning models using 🧠 Amazon SageMaker.

Jupyter Notebook 10,311 6,824 Updated Feb 19, 2025

Portable solution to generate genome alignment chains using lastz

Python 54 8 Updated Oct 11, 2024

BayerCLAW workflow orchestration system for AWS

Python 21 9 Updated Jun 25, 2024

R package for DNA methylation analysis

R 220 97 Updated Feb 12, 2025

Compute the Euler Characteristic Transform

Jupyter Notebook 12 2 Updated Oct 18, 2023

two-stage analysis of multi-environment trials for genomic selection and GWAS

R 22 5 Updated Feb 20, 2025

Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

R 1,137 84 Updated Jan 3, 2025

Easily Arrange Images with Patchwork Alongside ggplot2 Figures.

R 77 1 Updated Jan 22, 2025

Machine learning in Python with scikit-learn MOOC

Jupyter Notebook 1,163 530 Updated Jan 29, 2025

Software for painlessly estimating average nucleotide diversity within and between populations

Python 124 15 Updated Feb 21, 2025

genotype dimensionality reduction with a VAE

Python 43 9 Updated Apr 23, 2024

Methods for examining PCA locally along the genome.

HTML 76 13 Updated Aug 13, 2024
Roff 7 6 Updated Oct 19, 2019

Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

C++ 166 25 Updated Dec 19, 2024

Set of scripts to manupulate tab-delimited genotype calls files as well as to convert calls-files to other popular formats.

Python 10 2 Updated Jan 11, 2021
Shell 80 20 Updated Dec 19, 2023

Code and data to identify selection on traits controlled by many loci

HTML 7 6 Updated Apr 10, 2019

Variant discovery and genotyping pipelines from pangenome graphs

Python 5 5 Updated May 17, 2019

Tutorials on phylogenetic and phylogenomic inference

HTML 373 173 Updated Sep 13, 2023

Implementation of the multiple sequential markovian coalescent

D 87 20 Updated Nov 10, 2023

Plant phenotyping with image analysis

Python 691 267 Updated Feb 21, 2025

Studio Ghibli colour palettes

R 425 18 Updated Mar 18, 2024

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

Python 63 31 Updated Apr 25, 2024

Flight rules for git

42,010 3,196 Updated Aug 27, 2024

User guide for the qgg R package

1 Updated Jun 18, 2024

Statistical tools for Quantitative Genetic Analyses

R 36 7 Updated Jan 2, 2025

Atwell et al data

11 13 Updated Jan 16, 2019

Infer demographic history with the Moran model

Python 47 11 Updated Mar 25, 2024

Repository for the 2017 Genome Biology publication, "The interplay of demography and selection during maize domestication and expansion"

R 17 4 Updated Nov 24, 2020
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