Michael S. Cuoco's Projects
Conda recipes for the bioconda channel.
Automatically activate a conda environment when entering a folder with an environment.yml file
A cookiecutter template for computational biology projects
A boilerplate for reproducible computational biology projects.
A template for sequencing data storage and preprocessing.
My CV
Mike Cuoco's Curriculum Vitae
mike's shell, git, etc config files. also homebrew, migration setup. good stuff.
Practical understanding of approaches for dimension reduction of multi-dimensional datasets.
General-use computational environments for bioinformatics and computational biology
R scripts to find an authors publications on PubMed and BioRxiv and save to Biblatex
A structural variation pipeline for short-read sequencing
My general-use functions for bioinformatics
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
implements jackstraw methods in python test for significant PCs and associations between variables and PCs discovered in the data.
script and dotfiles for logging on to a new linux-based computed cluster
Personal website
Repository to host tool-specific module files for the Nextflow DSL2 community!
📄 A selection of minimal examples used to highlight R Markdown templates, as referred to in the "R Markdown Definitive Guide"
my-utils
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Analysis package for human LINE-1 targeted sequencing data obtained with SLAV-Seq protocol
My fork of JiekaiLab/scTE
R toolkit for single cell genomics