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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 the University of British Columbia with Sally Aitken and Sam Yeaman working on the CoAdapTree project. We're working on genomics-based approaches to assist four ecologically and economically important Canadian conifer species adapt in the face of changing climates, and we are (or will be) sharing every single line of code! Check out our GitHub page! See a summary of my public work for the CoAdapTree project.

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, creating basic maps, and more - check out my repo here

Contact

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

Pinned

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

    Python 1

  2. my custom modules

    Python

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

    Python 3 4

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

    Shell 2 2

  5. 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. Forked from brandonlind/testdata_validation

    Code to validate poolSeq data using indSeq data for comparison

    Jupyter Notebook 1

131 contributions in the last year

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Mon Wed Fri
Activity overview

Contribution activity

January 2022

Created 1 commit in 1 repository

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