The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.

compare results from GSEA and fGSEA

GPU utilization reporting for Slurm HPC clusters

Script for Epithelial and Immune single cell RNA-seq

Using stochastic block models for topic modeling

Code repository associated with the manuscript “Molecular and cellular cartography of the laboratory mouse using whole-body sections.”

Code related to analyses in Glasner, Rose, Sharma, et al Nature Immunology 2023.

Quantitative Allele Specific Analysis of Reads. Joint genotyping & ASE inference for RNA-seq data

Empirical Bayes GLM

Extending UNITY: Improved MCMC Sampling and Sample Overlap Correction for Joint Trait Analysis

Reworking of the Bash for HPC book into a class format

Multi-omics studies are available here

The package that sounds as it is called.

An Open Source Machine Learning Framework for Everyone

Code and data for fsusie paper.

Perf monitoring CLI tool for Apple Silicon

Fast Gene Set Enrichment Analysis

R package implementing methods for multivariate multiple regression with adaptive shrinkage priors.

Mixed-effects models in R using S4 classes and methods with RcppEigen

The online code repository for FASH (fashr).

R package for functional adaptive shrinkage (FASH).

R devel with ASAN / UBSAN sanitizers using clang/clang++

R configurations for Docker

'alto' is an R package that aligns topics from different LDA models, computes metrics for quantifying the goodness of alignment, and provides visualization functions to explore the alignment and ro…

R package for the analysis of massive SNP arrays.