A syntax-highlighting pager for git, diff, grep, rg --json, and blame output

LLM training in simple, raw C/CUDA

Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs

PredIG: an interpretable predictor of T-cell epitope immunogenicity

SpliceTransformer(SpTransformer) is a deep learning tool to predict tissue specific splicing site from pre-mRNA sequence

✂️ Deep learning-based splice site predictor that improves spliced alignments

Cell2Sentence: Teaching Large Language Models the Language of Biology

Check strandedness of RNA-Seq fastq files

GLM-4.5: Agentic, Reasoning, and Coding (ARC) Foundation Models

DeepSAP repository for documentation and supplemental data

FRASER - Find RAre Splicing Events in RNA-seq

conv_visualizer

PRedictor of IMmunogenic Epitopes

Lightweight coding agent that runs in your terminal

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available …

PyTorch code for Vision Transformers training with the Self-Supervised learning method DINO

An extremely fast Python linter and code formatter, written in Rust.

ImmunoVerse: A pan-cancer atlas of therapeutic T cell targets

Genome modeling and design across all domains of life

Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono

Official code repository for GATK versions 4 and up

Generates protein variant sequences based on imported mutations from VCF, MAF and additional files to generate a protein-variant database for use in proteogenomics studies

Accelerate the generation of personalized proteomes from a Variant calling format (VCF) file and a reference proteome using graphical processing units (GPUs).

Toolkit for processing sequences in FASTA/Q formats

Cutadapt removes adapter sequences from sequencing reads

A quality control analysis tool for high throughput sequencing data

A deep learning-based tool to identify splice variants

Models, design algorithms, and other software related to Salis lab publications

This repository contains implementations and illustrative code to accompany DeepMind publications