joreynajr

GIVE-UP

chromolooper

Chromatin loops can connect genetic elements together, this package attempt to do the same at the data-level and builds on tools such as pybedtools.

cmi-pb-challenge-winter-23-24

cmi-pb-momix

Applying jDR methods to CMI-PB

dchallenge

As the Ay Lab we are competing in the DChallenge where we are looking SNPs colocalizing for T1D and expression and integrating this with HiChIP interactions.

HiCnv

HiCnv is used to call copy number variations and breakpoints from Hi-C data

synapse_ontology

2016_OpenIntro

atacseq_ecdna_detection

Analyzing ATAC-seq data to find ecDNA

bioinformatics_references_detangled

Bioinformaticians take for granted so many standardized datasets. Let's pay more attention to those neat details.

mini-tutorials

Improving my linux practice through mini-tutorials

cdpipelines

Analysis pipelines.

chipline_example

Attempting to install and run the ChIPLine Pipelin

CMI-PB-mRNA-Module-Analysis-Tutorial

CMI-PB tutorial for contestants.

CSE-280a

Bioinformatics algorithms

dna_3d_structure

Testing DNA 3D structure software for PASTIS data

ECE269-Project

HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hic_loop_callers

Testing out various loop callers

joreynajr.github.io

pgltools

Paired Genomic Loci Tool Suite

plotgardener

Adding an additional GWAS-like plot

snakemake-best-practices

Personal best practices with Snakemake

snakemake-tutorial

Snakemake tutorial