This is the development home of the workflow management system Snakemake. For general information, see

Library to analyse, filter and plot MPRA count data.

With this snakemake pipeline you can process your MPRA sequencing data (assignment and count). It is the standard MPRA pipeline of the IGVF consortium and a further development of MPRAflow.

Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.

Main resource repository for the ISMB 2025 Tutorial IP2: Massively parallel reporter assays in functional regulatory genomics and as part of the IGVF data resource

The definitive list that answers "I want to do X in Python, which tool should I use?"

Snakemake pipeline for MPRA count processing

cfDNA analysis workflow

A tool to identify strand asymmetries in genomic data

Tool for extremely quick and customizable design of multi-allelic MPRA

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

R software library implementing the P-Net algorithm

Automated analysis and result reporting for targeted sequencing data

CADD scripts release for offline scoring. For more information about CADD, please visit our website

Analyse enhancer strength based on MPRA experiments.

Public facing deeplift repo

Deep Feature Interaction Maps (DFIM)

A modern Java library for working with (biological) ontologies.

Code to generate ontology annotated objects (e.g. HPO annotated patients)

A Tool to Annotate and Prioritize Exome Variants