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Bayer Crop Science
- mishaploid.github.io
- @mishaploid
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General tools for genomic analyses.
Example 📓 Jupyter notebooks that demonstrate how to build, train, and deploy machine learning models using 🧠 Amazon SageMaker.
Portable solution to generate genome alignment chains using lastz
BayerCLAW workflow orchestration system for AWS
Compute the Euler Characteristic Transform
two-stage analysis of multi-environment trials for genomic selection and GWAS
Color palette package in R inspired by works at the Metropolitan Museum of Art in New York
Easily Arrange Images with Patchwork Alongside ggplot2 Figures.
Machine learning in Python with scikit-learn MOOC
Software for painlessly estimating average nucleotide diversity within and between populations
Methods for examining PCA locally along the genome.
Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
Set of scripts to manupulate tab-delimited genotype calls files as well as to convert calls-files to other popular formats.
Code and data to identify selection on traits controlled by many loci
Variant discovery and genotyping pipelines from pangenome graphs
Tutorials on phylogenetic and phylogenomic inference
Implementation of the multiple sequential markovian coalescent
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.
Infer demographic history with the Moran model
Repository for the 2017 Genome Biology publication, "The interplay of demography and selection during maize domestication and expansion"