jr-leary7

SCISSORS

SCISSORS builds upon the Louvain graph-based clustering in Seurat by optimizing parameter selection when reclustering cell groups, with an eye towards identifying rare cell types.

scLANE

Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.

r

Bioinformatics analyses, class projects, etc. Mostly RMarkdown documents.

SurveyQuantReg

This repo contains an R package built to analyze NHANES survey data using quantile regression.

YehLabHTS

HTS Drug Discovery Analysis

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bash

Next generation sequencing pipelines that I've written.

bayesHVG

Identify highly variables genes in scRNA-seq data using Bayesian inference.

bayesVG

Identify variable genes in scRNA-seq and spatial transcriptomics data using Bayesian inference

cplusplus

C++ is misery, but in a good way

jackknife

My personal R package

quarto-site

My personal website

scLANE-Revision

code and data relating to the scLANE revision

brms

brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan

fastGEE

A fast(er) implementation of GEEs in R.

jr-leary7.github.io

PHC-6063-Modeling

Machine learning models for diabetes diagnoses

PHC-6088-Project

My PHC 6088 project for my MS program at UF.

PHC-6937-Project

My final project for PHC 6937 (Data Visualization) for my Biostatistics MS at UF.

python

My Python code. I used to hate Python, but recently I've been enjoying it more!

Qualifying-Exam

Notes for the 2024 UF Dept. of Biostatistic qualifying exam.

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

SCISSORS-Analyses

Analyses relating to the Yeh Lab's `SCISSORS` project

SCISSORS-Sims

Simulation study for SCISSORS

scLANE-Paper

analyses for the manuscript detailing `scLANE`

scLANE-Sims

Simulation studies for scLANE

scLANE-Simulations

Simulation study for the scLANE manuscript

SingleCell.jl

StatisticalRethinking

Working through McElreath's book on Bayesian statistics with R, Statistical Rethinking.