Code for improving the performance of sequence-to-expression models for making individual-specific gene expression predictions by fine-tuning them on personal genome and transcriptome data.

Analysis code for sc-veQTL study

NanoGPT (124M) in 5 minutes

DeepSEA implements in PyTorch

Build DeepSea training dataset from raw data

DeepSEA in TensorFlow

Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code.

Chromatin interaction aware gene regulatory modeling with graph attention networks

RNA-seq prediction with deep convolutional neural networks.

Saluki, a method to predict mRNA half-lives from sequence

Convolutional neural network analysis for predicting DNA sequence activity.

predicting expression effects of human genome variants ab initio from sequence

Sequential regulatory activity predictions with deep convolutional neural networks.

A collection of ML scripts to test the M1 Pro MacBook Pro

code to run sei and obtain sei and sequence class predictions

LLM101n: Let's build a Storyteller

Links to all data science, genomics, and other notes

scATAC-seq data analysis tools and papers

Making the community's best AI chat models available to everyone.

A curated list of resources for using LLMs to develop more competitive grant applications.

Awesome tmux-based terminal divider

Analysis for "Amiloride, an old diuretic drug, is a potential therapeutic agent for multiple myeloma"

A simple gene co-expression analyses workflow powered by tidyverse and graph analyses

MACS -- Model-based Analysis of ChIP-Seq

A short course on proteins and protein design aimed at early career students

TAD Calling using spectral clustering in R