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Jill V Hagey, MS, PhD |
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This is the home page of Jill Hagey's github |
Currently, I am a Bioinformatician in the Division of Healthcare Quality Promotion at the Centers for Disease Control and Prevention, where I am the bioinformatic domestic lead for the Antimicrobial Resistance Labortory Network. My team writes software, like PHoeNIx, to detect Antibiotic Resistance in Hospitial Associated Infections.
I got my PhD at the University of California, Davis in the Animal Biology Graduate Group with a designated emphasis in Host-Microbe Interactions. I am passionate about making "big data" in biology comprehensible and pretty. This home page will link you to my github projects. This page is still under construction 👷, but no hard hat needed. I currently write most of my work in python and R. Drop me a line if you find an error or have questions!
Check out my tutorials page!
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- Rumen Sampling Methods Bias Bacterial Communities Observed github page and paper.
- Fecal Microbiome of Dairy Cattle github page and the paper.
- Projects studying passive immunity in dairy calves:
- Determining how serum IgG is related to mortality in the first 4 months of life in dairy heifers
- Clinincal trial of plasma as a treatment for failure of passive transfer in dairy calves
- Evaluating the half-life of IgG from colstrum, colostrum replacer or bovine plasma
- Assesment of a commercial refractometer for onside evaluation of serum IgG and total milk solids
- Evalution of failure of passive transfer rates in calves either bottle or tube fed colostrum
- Utility scripts I have written that I use for a varity of projects are found here.
- 🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
- nf-core modules
- Containers for the Waterborne Diseases Prevention Branch at CDC.
- Technical Outreach and Assistance for States Team (TOAST) developed benchmark datasets for SARS-CoV-2 sequencing.
- Bioinformatics Chat podcast
- Bioinformatics Virtual Coordination Network
- Micro Binfie (Microbial Bioinformatics) Podcast
- Public Health Bioinformatics
- Public Health Alliance for Genomic Epidemiology (PHA4GE)
- StaPH-B (State Public Health Bioinformatics Workgroup and their Github
- 16S rRNA gene amplicon workflow from Holmes Lab
- Statistical Methods in Microbiome Research Workshop
- Happy Belly Bioinformatics
- Statistical Diversity Lab blog: Microbiome data analysis 101
- Modern Statistics for Modern Biology
- Statistical Rethinking: A Bayesian Course Using R and Stan
- Biomedical Data Science Text
- Resource Lists
- Examples and page with code.