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basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

basset

Convolutional neural network analysis for predicting DNA sequence activity.

chatgpt-demo

A demo repo based on OpenAI API (gpt-3.5-turbo)

chrombpnet

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

cisregmodels

Scripts for building computational models of gene regulation with tensorflow

cromwell_and_backend

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

dfim

Deep Feature Interaction Maps (DFIM)

dna2vec

dna2vec: Consistent vector representations of variable-length k-mers

dreammodel

evolution

This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'

fastism

In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.

fastqtl

Enhanced version of the FastQTL QTL mapper

hpoptim_example

johnchenresearch.github.io

Jekyll blog

maxatac

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

maxatac_pip_1.0.5

mosbat

Motif Similarity Based on Affinity of Targets

mpra_oligo_barcode_pipeline

mpramodel

reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

tamc

TAMC

tfmodisco

TF MOtif Discovery from Importance SCOres

tfmodisco-lite

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

tobias

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

variant-calling-pipeline-gatk4

Variant Calling Pipeline Using GATK4 and Nextflow

vision_transformer

warp