Fully local web research and report writing assistant

[NeurIPS2025] "AI-Researcher: Autonomous Scientific Innovation" -- A production-ready version: https://novix.science/chat

Integrated tool for prediction of potential neoantigens

A modular framework for multimodal cross-cell-type transcriptional regulation models

Addition to the Conditional Monge Gap to extend it to Chimeric Antigen Receptor T cell scRNAseq data

Biomni: a general-purpose biomedical AI agent

Reproducing GPT-2

This script demonstrates how to train a Cell2Sentence model from scratch using single-cell RNA-seq data. It includes all the working components from the notebook, with proper local model loading su…

Cell2Sentence: Teaching Large Language Models the Language of Biology

Protein Engineering via Exploration of an Energy Landscape

A deep learning-based tool to identify splice variants

Antibody Numbering and Antigen Receptor ClassIfication

Single cell analysis in the browser

Allows to score gene programs in Kinetic Trajectory datasets of CD8+ T cell differentiation to contextualize T cell gene programs and infer differentiation states (see Jaiswal et al Cancer Cell 202…

Get up and running with OpenAI gpt-oss, DeepSeek-R1, Gemma 3 and other models.

R package to read and write Parquet files

Material for Shiny Conf 2025 Workshop on Shiny performance

clinicaltrialr: Import study records from ClinicalTrials.gov

Tutorial on large language models for genomics

Files and code used to generate the CARTAR app to identify and validate CAR targets for cancer treatment.

Genome-scale design tool for oligo hybridization probes

A cross-platform proteomics data analysis suite