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Genome Institute of Singapore
- Singapore
- stuartlab.org
- https://orcid.org/0000-0002-3044-0897
- @timoast
Stars
Easy to maintain open source documentation websites.
gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
Visualize and annotate genomic coverage with ggplot2
A high-performance BigWig and BigBed library in Rust
Biological sequence analysis for the modern age.
Fast and Memory-Efficient Principal Component Analysis All in One
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
Visualizer for neural network, deep learning and machine learning models
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
Fast and memory-efficient exact attention
The full training script for Enformer - Tensorflow Sonnet
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
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.
R toolkit for the analysis of single-cell chromatin data
Fast alignment and preprocessing of chromatin profiles
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch