Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
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Updated
Mar 30, 2024 - Python
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
R package to accompany Time Series Analysis and Its Applications: With R Examples -and- Time Series: A Data Analysis Approach Using R
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
Sequence alignment tools
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
This bartender version could handle arbitrary length of barcode
Web application for designing DNA structures such as DNA origami.
Find and visualize rearrangements in DNA sequences
strataG is a toolkit for haploid sequence and multilocus genetic data summaries, and analyses of population structure.
🍶 Genome assembly with short sequence reads
Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
An efficient DNA sequence compressor using Neural Networks
Coronavirus genome analysis.
Deep neural networks implemented in TensorFlow & Python for predicting whether transcription factors will bind to given DNA sequences
Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification
Deep learning for identifying important motifs in DNA sequences. Exploration of the structure of the human genome by training neural network architectures (CNN, LSTM, Attention).
Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
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