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Achievement: YOLOAchievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor
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Achievements

Achievement: YOLOAchievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor
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@CoAdapTree @ModelValidationProgram
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brandonlind/README.md

Brandon Lind, Ph.D. - Integrative Life Sciences

interests - forest genomics • local adaptation • quantitative traits • population genetics • python

Hello, World! 👋 I'm currently a Research Fellow at Northeastern University with Katie Lotterhos using simulated data to assess machine learning methods for ranking population risk to climate change. I was formerly at the University of British Columbia with Sally Aitken and Sam Yeaman working on the CoAdapTree project to assist four ecologically and economically important Canadian conifer species adapt in the face of changing climates.

I've created several custom python functions for everyday use - eg using engines to parallelize reading in of large dataframes, submit/query/update slurm jobs and slurm queue, creating basic maps, and more - check out my repo here

Contact

✉️ lind.brandon.m@gmail.com
🐦 @iowensis
🎓 google scholar
🔬 research page
🔗 LinkedIn

Pinned

  1. CoAdapTree/pypoolation CoAdapTree/pypoolation Public

    python scripts for population genetic statistics for data coming out of the varscan pipeline

    Python 1

  2. pythonimports pythonimports Public

    my custom modules

    Python

  3. CoAdapTree/gatk_pipeline CoAdapTree/gatk_pipeline Public

    Pipeline for processing raw fastq files through SNP calling with GATK and subsequent filtering

    Python 3 4

  4. CoAdapTree/varscan_pipeline CoAdapTree/varscan_pipeline Public

    Pipeline for CoAdapTree to autonomously process raw fastq files through SNP calling with VarScan and subsequent filtering following bioinformatic best practices.

    Shell 2 3

  5. CoAdapTree/cmh_test CoAdapTree/cmh_test Public

    Forked from brandonlind/cmh_test

    This code takes output from the VarScan pipeline and calculates Cochran-Mantel-Haenszel chi-squared tests on stratified contingency tables of read counts standardized by population ploidy.

    Python

  6. CoAdapTree/testdata_validation CoAdapTree/testdata_validation Public

    Forked from brandonlind/testdata_validation

    Code to validate poolSeq data using indSeq data for comparison

    Jupyter Notebook 1