A Java API for high-throughput sequencing data (HTS) formats.

Application for making ENCODE Blacklists

sbt, the interactive build tool

A collection of unexpected stories involving emacs

MACS -- Model-based Analysis of ChIP-Seq

HoloLayer is a multimedia layer plugin designed specifically for Emacs

An emacs mode for interacting with scala sbt and projects

lsp-mode ❤️ metals

Sequential regulatory activity predictions with deep convolutional neural networks.

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.

Learning about Singularity (the container platform and not the technological singularity)

Single-cell analysis in Python. Scales to >1M cells.

Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share your research sources.

Automatic installation, usage, and fallback for tree-sitter major modes in Emacs 29

Shiny Interactive Web Apps for Single-Cell Data

Customize your Zotero workflow.

Lite wrapper of cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

ATAC-seq snakemake pipeline

AI-generated gene editing systems

Cookiecutter for snakemake slurm profile

Robust identification of perturbed cell types in single-cell RNA-seq data

Modern C++ Programming Course (C++03/11/14/17/20/23/26)

(R) Efficient methods and operators for the sparse matrix classes in 'Matrix' (esp. CSR format or "RsparseMatrix")

command-line optional argument parser

LD Score Regression (LDSC)

OS-Lib is a simple, flexible, high-performance Scala interface to common OS filesystem and subprocess APIs

Auto-format source code in many languages with one command

Use the world of Python from the comfort of Scala!

Emacs helper library (and minor mode) to work with conda environments

😈 Chagning cursor by mode for evil on terminal.