Michael S. Cuoco's repositories
general_functions
My general-use functions for bioinformatics
sz_slavseq
SLAV-seq analysis pipeline for SZ dataset
bioconda-recipes
Conda recipes for the bioconda channel.
cookiecutter-computational-biology
A boilerplate for reproducible computational biology projects.
cookiecutter-sequencing-data
A template for sequencing data storage and preprocessing.
michaelcuoco.com
Personal website
curriculum-vitae
My CV
dotfiles
mike's shell, git, etc config files. also homebrew, migration setup. good stuff.
ece204_project1
Practical understanding of approaches for dimension reduction of multi-dimensional datasets.
environments
General-use computational environments for bioinformatics and computational biology
FindMyPubs
R scripts to find an authors publications on PubMed and BioRxiv and save to Biblatex
gatk-sv
A structural variation pipeline for short-read sequencing
linux_setup
script and dotfiles for logging on to a new linux-based computed cluster
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
myutils
my-utils
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
pyslavseq
Analysis package for human LINE-1 targeted sequencing data obtained with SLAV-Seq protocol
seurat
R toolkit for single cell genomics
smartseq2
A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.
snakemake-workflow-template
A template for my snakemake workflows
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
souporcell
Clustering scRNAseq by genotypes
SQuIRE
Software for Quantifying Interspersed Repeat Expression
xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics