Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
R package to accompany Time Series Analysis and Its Applications: With R Examples -and- Time Series: A Data Analysis Approach Using R
VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
Sequence alignment tools
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
PlantCAD: cross-species modeling of plant genomes
Find and visualize rearrangements in DNA sequences
GenoArmory: A Unified Evaluation Framework for Adversarial Attacks on Genomic Foundation Models
A method to predict DNA shape features considering farther flanking region.
👾 Generate identicons for DNA sequences with Python
Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
Read DNA sequences from colourful Microsoft Word documents
Web application for designing DNA structures such as DNA origami.
Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification
GraphPart, a data partitioning method for ML on biological sequences
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