Fulbright Cátedra (August 2021)

This repository contains jupyter notbooks for fulbright Cátedra (symposium).

Requirements

• The requirements for these notebooks can be installed either directly using our specification file or by manually getting the required tools.

  • Our spec file is located in the github repository: (requiredPackages.txt). You can set up your environment using conda create -n fulbright --file requiredPackages.txt

  • Alternatively, you can also manually install the following packages to set up your environment. Most of the required packages can be obtained using conda as following

    • Let's get the jupyterlab using: conda install -c conda-forge jupyterlab

    • Plink: conda install -c bioconda plink

    • R on jupyterlba using: conda install -c r r-essentials r-irkernel

    • Don't forget to enable R in jupyter notebooks using IRkernel::installspec() in your R server.

    • You will also need the R packages: install.packages("tidyverse"), install.packages(dplyr), install.packages(plyr), install.packages(reshape2), & install.packages("vcfR")

    • VEP tool: conda install -c bioconda ensembl-vep

    • ADMIXTURE: conda install -c bioconda admixture

About the notebooks

These notebooks were created for Fulbright Cátedra (August 2021) and were meant to be used parallel to our presentation slides. These notebooks will guide your though most of the functionalities that are discussed during our presentations.

About the data

The raw data required for running the notebooks is present in the data/ folder. However, keeping the space constrains in mind, only the raw VCF files are shared. You will have to create the associated PED/BED files for processing manually. However, if you need any specific files, please reach out to us on email.

Live broadcasting video

Watch the YouTube video recorded live during the event here

Contact

Please contact king.jordan {-AT-} biology.gatech.edu for any queries/suggestions.

Acknowledgements

• Fulbright Colombia
• Augusto Valderrama-Aguirre, Universidad de Los Andes
• Leonardo Mariño-Ramírez, National Institute on Minority Health and Health Disparities, NIH
• Shivam Sharma, National Institute on Minority Health and Health Disparities, NIH
• King Jordan, Georgia Institute of Technology
• Shashwat Deepali Nagar, Georgia Institute of Technology