Making large AI models cheaper, faster and more accessible

Open source code for AlphaFold 2.

Uniform Manifold Approximation and Projection

AlphaFold 3 inference pipeline.

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Optimizing AlphaFold Training and Inference on GPU Clusters

Read-based phasing of genomic variants, also called haplotype assembly

Tool for plotting sequencing data along genomic coordinates.

List of gene lists for genomic analyses.

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

IDR

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities i…

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

Bhagavad Gita in JSON

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

phasing and Allele Specific Expression from RNA-seq

A template for standard compliant snakemake-workflows

A multi-gpu implementation of the self-organizing map in TensorFlow

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

A cookiecutter template for Snakemake workflows

AlphaLink2: Integrating crosslinking MS data into Uni-Fold-Multimer

ROSE: RANK ORDERING OF SUPER-ENHANCERS

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.

A comprehensive toolkit for mutational signature analysis

Singularity recipe for AlphaFold