mikecuoco

Ph.D. candidate in Bioinformatics and Systems Biology at UC San Diego.

University of California, San DiegoLa Jolla, CA

Pinned Repositories

BarcodeMate
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bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0 00
bisb-bootcamp-2020-module08
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BloodBrainClassifier
Language:Jupyter Notebook2 2 00
cluster_dotfiles
Language:Vim Script0 2 10
conda-auto-env
Automatically activate a conda environment when entering a folder with an environment.yml file
Language:Shell0 1 00
cookiecutter-compbio
A cookiecutter template for computational biology projects
Language:Python0 0 00
general_functions
My general-use functions for bioinformatics
Language:Shell1 2 00
michaelcuoco.com
Personal website
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sz_slavseq
SLAV-seq analysis pipeline for SZ dataset
Language:Jupyter Notebook1 1 430

mikecuoco's Repositories

mikecuoco/BloodBrainClassifier
Language:Jupyter Notebook2 2 00
mikecuoco/general_functions
My general-use functions for bioinformatics
Language:Shell1 2 00
mikecuoco/sz_slavseq
SLAV-seq analysis pipeline for SZ dataset
Language:Jupyter Notebook1 1 430
mikecuoco/BarcodeMate
Language:Python0 0 00
mikecuoco/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0 00
mikecuoco/cluster_dotfiles
Language:Vim Script0 2 10
mikecuoco/cookiecutter-computational-biology
A boilerplate for reproducible computational biology projects.
Language:Shell00
mikecuoco/cookiecutter-sequencing-data
A template for sequencing data storage and preprocessing.
Language:Python0 2 00
mikecuoco/michaelcuoco.com
Personal website
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mikecuoco/curriculum-vitae
My CV
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mikecuoco/cv
Mike Cuoco's Curriculum Vitae
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mikecuoco/dotfiles
mike's shell, git, etc config files. also homebrew, migration setup. good stuff.
Language:Vim script1 0
mikecuoco/ece204_project1
Practical understanding of approaches for dimension reduction of multi-dimensional datasets.
Language:Jupyter Notebook1 0
mikecuoco/environments
General-use computational environments for bioinformatics and computational biology
2 0
mikecuoco/FindMyPubs
R scripts to find an authors publications on PubMed and BioRxiv and save to Biblatex
Language:TeX2 0
mikecuoco/gatk-sv
A structural variation pipeline for short-read sequencing
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mikecuoco/GraffiTE
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.
Language:R0 0
mikecuoco/kitchen_recipes
mikecuoco/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
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mikecuoco/myutils
my-utils
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mikecuoco/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Language:Python0 0
mikecuoco/pyslavseq
Analysis package for human LINE-1 targeted sequencing data obtained with SLAV-Seq protocol
Language:Python1 3
mikecuoco/scTE
My fork of JiekaiLab/scTE
Language:Jupyter Notebook1 1
mikecuoco/seurat
R toolkit for single cell genomics
Language:R0 0
mikecuoco/snakemake-workflow-template
A template for my snakemake workflows
Language:Python1
mikecuoco/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
Language:CAP CDS
mikecuoco/souporcell
Clustering scRNAseq by genotypes
Language:Python1 3
mikecuoco/SQuIRE
Software for Quantifying Interspersed Repeat Expression
Language:Python1 0
mikecuoco/tebreak
Find and characterise transposable element insertions
mikecuoco/xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
Language:Python0 0