FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

Helper scripts for biological data processing from Sentieon

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

DNA foundation modeling from molecular to genome scale

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

pandas on AWS - Easy integration with Athena, Glue, Redshift, Timestream, Neptune, OpenSearch, QuickSight, Chime, CloudWatchLogs, DynamoDB, EMR, SecretManager, PostgreSQL, MySQL, SQLServer and S3 (…

A novel genome assembly pipeline based on deep learning

Kolmogorov Arnold Networks

LoFreq Star: Sensitive variant calling from sequencing data

Make awesome display tables using Python.

Single-cell analysis methods in Rust

A modern, high customizable, responsive Jekyll theme for documentation with built-in search.

Burn is a new comprehensive dynamic Deep Learning Framework built using Rust with extreme flexibility, compute efficiency and portability as its primary goals.

a minimal, scriptable genome browser for python

Lecture Notes for Linear Algebra Featuring Python. This series of lecture notes will walk you through all the must-know concepts that set the foundation of data science or advanced quantitative ski…

Python wrapper for wavefront alignment using WFA2-lib

A Collection of Variational Autoencoders (VAE) in PyTorch.

Tool for plotting sequencing data along genomic coordinates.

Simple pileup-based variant caller

Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium. These files can be used as standard resource of BED files …

Dermatology ddx dataset, Jax implementations of Monte Carlo conformal prediction, plausibility regions and statistical annotation aggregation from our recent work on uncertain ground truth (TMLR'23…

Ultima scripts related to downstream processing of WGS, MRD, methylation analysis

Various algorithms for analysing genomics data

Implementation of C++ standard libraries in C

Fast random access of gzip files in Python

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

markov clustering in python

Wang Yi's GPT solution

MLX: An array framework for Apple silicon