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deep learning-inspired explainable sequence model for transcription initiation

Python 93 8 Updated Nov 7, 2024
Jupyter Notebook 17 4 Updated Oct 21, 2024

The official Meta Llama 3 GitHub site

Python 27,965 3,203 Updated Aug 12, 2024

Biological foundation modeling from molecular to genome scale

Jupyter Notebook 1,245 152 Updated Dec 18, 2024

Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.

Jupyter Notebook 42,192 4,532 Updated Jan 18, 2025

Complete assemblies of non-human primate genomes

40 3 Updated Oct 14, 2024

Package to Score Sequences using Rule Set 3

Jupyter Notebook 11 Updated Feb 24, 2024

A flexible and fast sgRNA counter from FASTQ Files

Rust 9 1 Updated Oct 31, 2024

Analysis code and results for dreamlet

R 9 1 Updated May 31, 2024

Code associated with the paper titled "A high-performance neuroprosthesis for speech decoding and avatar control" , published in Nature in 2023.

Jupyter Notebook 64 4 Updated Aug 23, 2023

Integrated Differential Expression and Annotation

HTML 4 Updated Nov 22, 2024

MS Word template for styling a manuscript for a bioRxiv submission

35 7 Updated Feb 11, 2019

R package implementation of Milo for testing for differential abundance in KNN graphs

R 350 23 Updated Nov 20, 2024

A tool to perform cluster enrichment/depletion analyses

Python 2 Updated Nov 26, 2024

Framework for sensitive DE testing (using neighbourhoods)

R 63 3 Updated Jul 20, 2024
Jupyter Notebook 6 1 Updated Apr 25, 2023

Draw UpSet plots with Matplotlib

Python 333 65 Updated May 2, 2024

Single-cell epigenomics analysis tools

Python 244 28 Updated Dec 28, 2024
Jupyter Notebook 34 3 Updated Sep 5, 2024

Jupyter notebooks for the Natural Language Processing with Transformers book

Jupyter Notebook 3,974 1,258 Updated Aug 21, 2024

scPerturb: A resource and a python/R tool for single-cell perturbation data

Jupyter Notebook 110 7 Updated Aug 26, 2024

Code for evaluation of differential expression methods in single-cell RNA-seq data

R 111 27 Updated Aug 13, 2020

Code for reproducing "Exploring genetic interaction manifolds constructed from rich single-cell phenotypes"

Jupyter Notebook 50 22 Updated Jun 6, 2020

Code associated with tafka-crisprQTL (Gasperini, et al. 2019)

R 3 1 Updated Jul 27, 2020

pseudobulking on an AnnData object

Python 28 1 Updated Jun 30, 2023

Neural Networks: Zero to Hero

Jupyter Notebook 12,718 1,731 Updated Aug 18, 2024

Code and examples for JHU Computational Genomics class

Jupyter Notebook 296 112 Updated Oct 22, 2024

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Java 993 371 Updated Jan 13, 2025

Detecting sites of genomic enrichment

C 190 27 Updated May 8, 2023
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