Adam Youlin He's repositories
borzoi_qtls
Curated QTLs used in the Borzoi paper.
bpnet-lite
This repository hosts a minimal version of a Python API for BPNet.
DeepExplain
A unified framework of perturbation and gradient-based attribution methods for Deep Neural Networks interpretability
dREG
Detecting Regulatory Elements using GRO-seq and PRO-seq
elemeNT_core_promoter_pwms
More accessible dump of the PWMs from ElemeNT (10.1080/21541264.2015.1067286)
enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
ExP-model-fit
Example code for fitting the ExP model from Bergman et al. 2022
LearningX
Deep & Classical Reinforcement Learning + Machine Learning Examples in Python
mac-dev-playbook
Mac setup and configuration via Ansible.
nascent_RNA_models
Repository for modeling PRO-cap data with BPNet.
persona5_calculator
A tool to help calculate fusions in Persona 5.
proseq2.0
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing
tangermeme
Biological sequence analysis for the modern age.
tfmodisco-lite
A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
ukbb_parser
A Python module for loading phenotypic and genetic data from the UK Biobank.
webinars
Training material based on webinar events