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.
PlantCAD: cross-species modeling of plant genomes
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
Find and visualize rearrangements in DNA sequences
A method to predict DNA shape features considering farther flanking region.
👾 Generate identicons for DNA sequences with Python
Web application for designing DNA structures such as DNA origami.
Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
GenoArmory: A Unified Evaluation Framework for Adversarial Attacks on Genomic Foundation Models
GraphPart, a data partitioning method for ML on biological sequences
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
Read DNA sequences from colourful Microsoft Word documents
This bartender version could handle arbitrary length of barcode
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