Spec-Bench: A Comprehensive Benchmark and Unified Evaluation Platform for Speculative Decoding (ACL 2024 Findings)

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Modelling human health trajectories using generative transformers

Official code repository for GATK versions 4 and up

Open-source implementation of AlphaEvolve

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

A playbook for systematically maximizing the performance of deep learning models.

Pytorch implementation of set transformer

This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.

a framework for training sequence-level deep learning networks

code to run sei and obtain sei and sequence class predictions

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

Various algorithms for analysing genomics data

Predictive Biomarker Modeling Framework (PBMF)

A Hyperparameter Tuning Library for Keras

A small library for automatical adjustment of text position in matplotlib plots to minimize overlaps.

Pangolin is a deep-learning method for predicting splice site strengths.

Specifications of SAM/BAM and related high-throughput sequencing file formats

Genomic VCF to tab-separated values

GDC Data Transfer Tool

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

Bioinformatics code libraries and scripts

add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot

A simple and efficient tool to parallelize Pandas operations on all available CPUs

annotate a VCF with other VCFs/BEDs/tabixed files

CADD scripts release for offline scoring. For more information about CADD, please visit our website

add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.

dN/dS methods to quantify selection in cancer and somatic evolution

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.