philippmuench

dna_lstm

LSTM for binary DNA sequence classification

PMtools

Helper function for comparative genomics and metagenomics

eden

EDEN: evolutionary dynamics within environments

omm-antibiotics2022

Code to reproduce Münch et al. 2022 Manuscript "Pulsed antibiotic treatments of gnotobiotic mice manifests in complex community dynamics and resistance effects"

auspice

Web app for visualizing pathogen evolution

bowtie2_classification

A command-line tool for performing efficient genome sequence alignment. It includes scripts to build bowtie2 index from multiple fasta files and to perform sequence alignment in a sliding window manner, reporting the number and percentage of successful alignments to specified databases.

clean-theme-obsidian

Minimal theme for Obsidian

create-react-app-auth-amplify

Implements a basic authentication flow for signing up/signing in users as well as protected client side routing using AWS Amplify.

crispr2020

https://huttenhower.sph.harvard.edu/crispr2020/ datasets downloads

deepG

DeepG, or 'Deep Genomics', is a R library which allows you to train and apply deep neural networks on genomic datasets

docker-stacks

Ready-to-run Docker images containing Jupyter applications

docs

Documentation site for OpenFaaS

eden_ui

the user interface for EDEN - Evolutionary Dynamics within Environments

ggplot2

An implementation of the Grammar of Graphics in R

HaplotypeDeconstructor

jobson

A platform for transforming command-line applications into a job service.

jsPsych

A JavaScript library for creating and running behavioral experiments in a web browser

k-mer-plot

mkdocs-demo

MkDocs Demo

mkdocs-material

A Material Design theme for MkDocs

mlrMBO

Toolbox for Bayesian Optimization and Model-Based Optimization in R

Obsidian-Monokai

Monokai theme for Obsidian

OligoMM-facilities

code to reproduce figure 7

OligoMM-report

OligoMMR

R library for OligoMM data analysis

roam-css-styles

Visually polished CSS styles for RoamResearch

roam_darktheme

A dark theme for Roam Research

shiny

simon-project-1

tensorflow-statereader

This repository provides scripts to train an LSTM and then extract states from it in Tensorflow.