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dna-sequences

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lucidrains /enformer-pytorch

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

deep-learning genomics gene-expression artificial-intelligence transformer attention-mechanism dna-sequences

UpdatedJul 7, 2025
Python

helicalAI /helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

bioinformatics rna-seq deep-learning biology gene-expression vcf artificial-intelligence transformer rnaseq rna dna-sequences uce evo2 pre-training pre-trained-model foundation-models scgpt geneformer transcriptformer helixmrna

UpdatedDec 16, 2025
Python

nickpoison /astsa

R package to accompany Time Series Analysis and Its Applications: With R Examples -and- Time Series: A Data Analysis Approach Using R

package data-science r data-analysis missing-data kalman-filter em-algorithm dna-sequences time-series-analysis state-space-models astsa

UpdatedDec 15, 2025
R

Griffan /VerifyBamID

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

bioinformatics genetics next-generation-sequencing biostatistics bam qc-analysis dna-sequences contamination cram

UpdatedMay 21, 2024
mupad

OpenHero /gblastn

G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

bioinformatics gpu high-performance cuda nvidia dna high-performance-computing dna-sequences ncbi-blast blastn dna-alignment

UpdatedOct 20, 2022
C++

BioJulia /BioAlignments.jl

Sequence alignment tools

bam-files bioinformatics biology high-throughput-sequencing dna-sequences sequence-alignment sequence-analysis biojulia smith-waterman-alignment sam-files

UpdatedAug 7, 2024
Julia

muellan /metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

bioinformatics genome taxonomy metagenomics classification fasta fastq metagenomes dna-sequences short-read-mapper read-mapping metagenomic-analysis metagenomic-classification genomic-data-analysis bioinformatics-algorithms long-reads metagenomic-data refseq ncbi-refseq bioinformatics-tool

UpdatedMay 26, 2025
C++

plantcad /plantcad

PlantCAD: cross-species modeling of plant genomes

dna-sequences angiosperms deleterious-mutation mamba-state-space-models dna-language-models

UpdatedDec 1, 2025
Python

smortezah /smashpp

Find and visualize rearrangements in DNA sequences

data-visualization high-throughput-sequencing dna-sequences alignment-free genome-rearrangment genome-compression

UpdatedDec 1, 2025
C++

dputhier /pygtftk

A python package and a set of shell commands to handle GTF files

bioinformatics gene rna-seq genomics cds ngs tts transcript bigwig chip-seq gtf bed exon tss dna-sequences genomic intron splicing

UpdatedDec 11, 2025
Python

jvrana /benchling-api

A python wrapper for the benchling api

dna api-wrapper dna-sequences

UpdatedSep 11, 2020
Python

JinsenLi /deepDNAshape

A method to predict DNA shape features considering farther flanking region.

dna dna-sequences dna-structures

UpdatedSep 25, 2024
Python

Edinburgh-Genome-Foundry /sequenticon

👾 Generate identicons for DNA sequences with Python

synthetic-biology lims dna-sequences sequence-editing

UpdatedMay 8, 2025
Python

MAGICS-LAB /GenoArmory

GenoArmory: A Unified Evaluation Framework for Adversarial Attacks on Genomic Foundation Models

visualization benchmark dna safety vulnerability defence quantization dna-sequences adversarial-attacks adversarial-training

UpdatedSep 20, 2025
Python

xzx0554 /EVO2-Virus

A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence

bioinformatics virus metagenomics dna rnaseq rna dna-sequences evo2

UpdatedMar 28, 2025
Python

debbiemarkslab /variational-synthesis

Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).

generative-model protein-sequences dna-sequences experimental-design

UpdatedFeb 17, 2022
Python

Edinburgh-Genome-Foundry /crazydoc

Read DNA sequences from colourful Microsoft Word documents

bioinformatics synthetic-biology molecular-biology dna-sequences computer-aided-design

UpdatedMay 12, 2025
Python

UC-Davis-molecular-computing /scadnano

Web application for designing DNA structures such as DNA origami.

dna-sequences cadnano dna-origami dna-structures

UpdatedDec 15, 2025
Dart

QData /ChromeGCN

Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

genomics dna hi-c dna-sequences graph-convolutional-networks graph-neural-networks

UpdatedFeb 2, 2021
Python

graph-part /graph-part

GraphPart, a data partitioning method for ML on biological sequences

machine-learning bioinformatics protein-sequences dna-sequences train-test-split

UpdatedOct 26, 2023
Jupyter Notebook

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