Trevor Freeman's repositories
ngs
A Nextflow pipeline for base NGS analysis.
quarto-book
A basic quarto book template.
SRAlign
a flexible pipeline for short read alignment to a reference
SRAtac
A pipeline for ATAC-seq preprocessing, alignment, peak calling, and read counting. Built on the SRAlign pipeline.
SRAlign-test
A central set of files for reproducible testing of SRAlign and pipelines built on SRAlign.
fetch-sra-fastq
Fetch fastq files from SRA
bioinformatics_algorithms
Notes and solutions for Bioinformatics Algorithms 3rd ed. by Compeau and Pevzner.
biofx_python
Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
head-first-design-patterns
Code examples from Head First Design Patterns.
flask-tutorial
The official Flask tutorial at https://flask.palletsprojects.com/en/2.2.x/tutorial/
cfb_pickem
Pick college football games against the spread!
cookiecutter-data-science
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
flask_blog
A simple Flask blog application from a code along tutorial by Corey Schafer
cfb_rankings_analysis
Analyze historical rankings and ratings for college football teams.
cookiecutter-pypackage
Cookiecutter template for a Python package.
biomed-exercises
Exercises for Candidates to join the BioMedical Team
SRAlign-template
A template for a project using SRAlign or a pipeline built on SRAlign.
atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
docker
A collection of Dockerfiles for my most useful base images
tiny_python_projects
Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.