neevor

SimPhy

SimPhy: A comprehensive simulator of gene family evolution

hyena-dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

spacetime

Code for SpaceTime 🌌⏱️. Proposed in Effectively Modeling Time Series with Simple Discrete State Spaces, ICLR 2023.

WITCH-NG

phylter

Detection of outlier genes and species in phylogenomics

LTEE-Ecoli

Genomics resources for the Long-Term Evolution Experiment with E. coli

amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

mathlib4

The math library of Lean 4

resistomeanalyzer

Prodigal

Prodigal Gene Prediction Software

ARGs_and_Diet

Scripts and docker images used in paper: Association of diet and antimicrobial resistance in healthy US adults

ARG_metagenome

Metagenomic analysis workflow for the identification and quantification of antimicrobial resistance genes (ARG) from human stool samples..

cdc-file-transfer

Tools for synching and streaming files from Windows to Linux

requests

A simple, yet elegant, HTTP library.

mathlib3

Lean 3's obsolete mathematical components library: please use mathlib4

build-your-own-x

Master programming by recreating your favorite technologies from scratch.

mechanica

Interactive, particle-based physics, chemistry and biology modeling and simulation environment

LARRY

awesome-code-review

An "Awesome" list of code review resources - articles, papers, tools, etc

FASTK

A fast K-mer counter for high-fidelity shotgun datasets

fpm

Fortran Package Manager (fpm)

dyngen

Simulating single-cell data using gene regulatory networks 📠

single-cell

A collection of documents that reflect various design decisions that have been made for the cellxgene project.

manuscript_ab_epitope_interaction

PyTCP

PyTCP is a fully functional TCP/IP stack written in Python. It supports TCP stream-based transport with reliable packet delivery based on a sliding window mechanism and basic congestion control. It also supports IPv6/ICMPv6 protocols with SLAAC address configuration. It operates as a user space program attached to the Linux TAP interface.

mamba

The Fast Cross-Platform Package Manager

reproducible_research

A template repository for how I structure my scientific research

human_impacts

FAVITES

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

spheres-augur-build

This repository analyzes viral genomes using Nextstrain to understand how SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, evolves and spreads. This is a copy of the original Nextstrain ncov repository, which will (by default) build augur all 50 states + DC + PR using the same parameters and subsampling strategy.