Stars
deep learning-inspired explainable sequence model for transcription initiation
Biological foundation modeling from molecular to genome scale
Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.
A flexible and fast sgRNA counter from FASTQ Files
Analysis code and results for dreamlet
Code associated with the paper titled "A high-performance neuroprosthesis for speech decoding and avatar control" , published in Nature in 2023.
MS Word template for styling a manuscript for a bioRxiv submission
R package implementation of Milo for testing for differential abundance in KNN graphs
A tool to perform cluster enrichment/depletion analyses
Framework for sensitive DE testing (using neighbourhoods)
Jupyter notebooks for the Natural Language Processing with Transformers book
scPerturb: A resource and a python/R tool for single-cell perturbation data
Code for evaluation of differential expression methods in single-cell RNA-seq data
Code for reproducing "Exploring genetic interaction manifolds constructed from rich single-cell phenotypes"
Code associated with tafka-crisprQTL (Gasperini, et al. 2019)
Neural Networks: Zero to Hero
Code and examples for JHU Computational Genomics class
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.