timoast

Tim Stuart's starred repositories

netron

Visualizer for neural network, deep learning and machine learning models

Language:JavaScriptMIT27811 300 1138

flash-attention

Fast and memory-efficient exact attention

Language:PythonBSD-3-Clause13715 114 1059

dlwpt-code

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

Language:Jupyter Notebook4717 112 109

bioicons

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

Language:VueMIT1323 17 44

gget

🧬 gget enables efficient querying of genomic reference databases

Language:PythonBSD-2-Clause933 11 68

hts-specs

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

Language:TeX647 100 430

rig

The R Installation Manager

Language:RustMIT631 9 200

ffq

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

Language:PythonMIT545 13 50

noodles

Bioinformatics I/O libraries in Rust

Language:RustMIT488 22 219

nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Language:PythonNOASSERTION455 22 54

enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Language:PythonMIT419 17 36

signac

R toolkit for the analysis of single-cell chromatin data

Language:RNOASSERTION324 6 1211

ggcoverage

Visualize and annotate genomic coverage with ggplot2

Language:RNOASSERTION227 5 32

chromap

Fast alignment and preprocessing of chromatin profiles

Language:C++MIT189 7 107

tangermeme

Biological sequence analysis for the modern age.

Language:PythonMIT178 10 12

BPCells

Scaling Single Cell Analysis to Millions of Cells

Language:C++NOASSERTION152 4 96

chrombpnet

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

Language:Jupyter NotebookMIT115 38 125

tf-bind-transformer

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

Language:PythonMIT81 80

vsn-pipelines

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

Language:NextflowGPL-3.074 12 204

seq_io

FASTA and FASTQ parsing in Rust

Language:RustMIT69 5 12

bigtools

A high-performance BigWig and BigBed library in Rust

Language:RustMIT65 3 17

learning_docker

Learning about Docker.

Language:DockerfileMIT52 5 2

PCAone

Fast and Memory-Efficient Principal Component Analysis All in One

Language:C++GPL-3.039 7 5

splitcode

Flexible and efficient parsing, interpreting and editing of sequencing reads

Language:CBSD-2-Clause38 3 23

CellSpace

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

Language:C++MIT31 1 6

AMULET

A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.

Language:PythonGPL-3.029 4 24

gget_examples

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

Language:Jupyter NotebookBSD-2-Clause26 4 2

enformer-tensorflow-sonnet-training-script

The full training script for Enformer - Tensorflow Sonnet

Language:PythonApache-2.016 2 2

scifiRNA-seq_publication

The million-scale method for single-cell analysis

Language:Jupyter Notebook10 18 2

Volans

:tropical_fish: A fast pipeline to preprocess the ATAC-seq data.

Language:RustBSD-3-Clause3 2 1