Software package to design bridge RNAs as described by Durrant & Perry et al.

An efficient CLI to extract sequences from the SRA

Universal Single-Cell Genomics Preprocessing package

LLM agents for working with the SRA and associated bioinformatics databases.

Easy to maintain open source documentation websites.

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

Bioinformatics I/O libraries in Rust

Visualize and annotate genomic coverage with ggplot2

A high-performance BigWig and BigBed library in Rust

Biological sequence analysis for the modern age.

Fast, Accurate and Memory-Efficient Principal Component Analysis For Tera-scale Dataset

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

Visualizer for neural network, deep learning and machine learning models

Foundation Models for Genomics & Transcriptomics

Learning about Docker.

Scaling Single Cell Analysis to Millions of Cells

Fast and memory-efficient exact attention

The full training script for Enformer - Tensorflow Sonnet

The R Installation Manager

Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace

A tool to find sequencing data and metadata from public databases.

🧬 gget enables efficient querying of genomic reference databases

Examples for gget (https://github.com/pachterlab/gget).

Flexible and efficient parsing, interpreting and editing of sequencing reads

🐠 A fast pipeline to preprocess the ATAC-seq data.

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

A repository of pipelines for single-cell data in Nextflow DSL2

A library of free open source icons for science illustrations in biology and chemistry

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

Code for the book Deep Learning with PyTorch by Eli Stevens, Luca Antiga, and Thomas Viehmann.