trev-f Goto Github PK

apptainer-images

atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

biofx_python

Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)

bioinformatics_algorithms

Notes and solutions for Bioinformatics Algorithms 3rd ed. by Compeau and Pevzner.

biomed-exercises

Exercises for Candidates to join the BioMedical Team

bovine_rnaseq_trial

cfb_pickem

Pick college football games against the spread!

cfb_rankings_analysis

Analyze historical rankings and ratings for college football teams.

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

cookiecutter-pypackage

Cookiecutter template for a Python package.

docker

A collection of Dockerfiles for my most useful base images

fetch-sra-fastq

Fetch fastq files from SRA

flask-tutorial

The official Flask tutorial at https://flask.palletsprojects.com/en/2.2.x/tutorial/

flask_blog

A simple Flask blog application from a code along tutorial by Corey Schafer

hands_on_ml

head-first-design-patterns

Code examples from Head First Design Patterns.

hello-nf

ngs

A Nextflow pipeline for base NGS analysis.

quarto-book

A basic quarto book template.

rnaseq-crash-course

sralign

a flexible pipeline for short read alignment to a reference

sralign-template

A template for a project using SRAlign or a pipeline built on SRAlign.

sralign-test

A central set of files for reproducible testing of SRAlign and pipelines built on SRAlign.

sratac

A pipeline for ATAC-seq preprocessing, alignment, peak calling, and read counting. Built on the SRAlign pipeline.

tiny_python_projects

Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.