GAME was designed for the functional genomics community to create seamless communication across pre-trained models and genomics datasets. It is a product of the feedback from many model and dataset…

Biological sequence analysis for the modern age.

A suite of tools for machine learning with genomics data

Code for data analysis and processing of Brennan et al regarding Zelda's role as a pioneer.

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

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

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

Hyper-parameter optimization for Keras

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

A repository for explaining feature attributions and feature interactions in deep neural networks.

Motif benchmarking supplementary data for paper submission

Raster geoms for ggplot2

ChExAlign: alignment and quantification of ChIP-exo crosslinking patterns

An R package for statistical quality control of ChIP-exo/nexus data.

Deep Feature Interaction Maps (DFIM)

Publication-quality sequence logos in R

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

ChIP-nexus pipeline

Performant Pythonic GenomicRanges

Tracking ML experiments using gin-config, wandb, comet.ml and S3.

A unified framework of perturbation and gradient-based attribution methods for Deep Neural Networks interpretability

Application for making ENCODE Blacklists

Multi-sample multi-group scRNA-seq analysis tools

IDR

Simple and efficient access to genomic data for deep learning models.

Visualizing Star Wars scripts with arc diagrams