Containerized cancer subtype prediction tools for gene expression, miRNA, DNA methylation, somatic mutations and copy number variation.

Detecting methylation using signal-level features from Nanopore sequencing reads

An Open Source YouTube app for privacy

Benchmarking of the Methylationcaller for Nanopore Sequencing data (Bachelor thesis Marvin Mayer)

Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping

A pipeline that accurately simulates high quality publicly cancer genomes (VCFs, CNAs and SVs).

Single cell omics biology annotations

This is the official repository for HypoGeniC (Hypothesis Generation in Context) and HypoRefine, which are automated, data-driven tools that leverage large language models to generate hypothesis fo…

Metagenomic Estimation of Dietary Intake and Content.

Easy Metagenome Pipeline

COBRApy is a package for constraint-based modeling of metabolic networks.

An AI-powered research assistant that performs iterative, deep research on any topic by combining search engines, web scraping, and large language models. The goal of this repo is to provide the si…

Tutorial on large language models for genomics

Tools for plotting methylation data in various ways

A package to run real time analysis of nanopore methylation data.

Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.

DegenPrimer is a tool to check the quality of degenerate primers by simulating PCR

A straightforward and complete next-generation sequencing read simulator

Fragment End Integrated Analysis tool

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

ARGfore: A multivariate time-series forecasting framework for predicting abundance of antibiotic resistance genes

quickly filter fastq files by matching sequences to a set of regex patterns

Toolkit for copy number analysis of low-pass WGS data. Includes an implementation of PlasmaSeq

A high-throughput ichorCNA pipeline compatible with human and animal genomes

Sturgeon is a CNS neural network classifier

Rust bindings to minimap2 library

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat

This pipeline is designed to take you from raw exome sequencing data all the way to meaningful variant discovery.