A method to predict DNA shape features considering farther flanking region.
☆40Sep 25, 2024Updated last year
Alternatives and similar repositories for deepDNAshape
Users that are interested in deepDNAshape are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Geometric deep learning of protein–DNA binding specificity☆78Mar 19, 2025Updated last year
- Interpretable bimodal network for transcription factors binding site prediction☆10Jun 29, 2023Updated 2 years ago
- ☆10Jan 19, 2019Updated 7 years ago
- ☆34Jan 27, 2025Updated last year
- Recurrent Variational Auto gene encoder☆19Jan 12, 2023Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆13Apr 7, 2023Updated 3 years ago
- 📦 A Command Line Tool for downloading protein structures, sequences and MSAs☆10Nov 21, 2017Updated 8 years ago
- R package for high-throughput DNA shape predictions and feature encoding☆20Jul 1, 2021Updated 4 years ago
- A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and buildin…☆27Jul 15, 2025Updated 10 months ago
- RoseTTAFold2 protein/nucleic acid complex prediction☆380Jun 3, 2024Updated last year
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆13Oct 16, 2025Updated 7 months ago
- A Xojo/python tool for identification and annotation of transcription factor binding sites in bacterial genomes☆19Jan 16, 2026Updated 4 months ago
- Code from "Deep Learning Of The Regulatory Grammar Of Yeast 5′ Untranslated Regions From 500,000 Random Sequences"☆16Sep 26, 2017Updated 8 years ago
- fastest GTF/GFF-to-BED converter chilling around☆32Mar 19, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Pipeline for eukaryotic genome annotation based on external evidences☆14Feb 23, 2023Updated 3 years ago
- Python package to run DefensePredictor, a model that identifies proteins involved in anti-phage defense☆51Apr 27, 2026Updated 3 weeks ago
- ☆13Jul 5, 2019Updated 6 years ago
- code to run sei and obtain sei and sequence class predictions☆114Dec 20, 2022Updated 3 years ago
- Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.☆18Jan 14, 2025Updated last year
- ☆15Nov 11, 2019Updated 6 years ago
- ☆21Mar 20, 2017Updated 9 years ago
- Collection of tools to retrieve siRNA (small interfering RNA) candidate sequences targeting your gene of interest from popular siRNA desi…☆20Nov 22, 2022Updated 3 years ago
- An introductory workshop to protein language models☆17May 24, 2022Updated 4 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- ☆11Feb 6, 2023Updated 3 years ago
- A collection of command-line tools I wrote to make various repetitive tasks more convenient☆16May 17, 2026Updated last week
- AptaNet as a Deep Learning approach for Aptamer-Protein Interaction Prediction☆28Jun 15, 2021Updated 4 years ago
- ☆10Dec 12, 2017Updated 8 years ago
- HMmer Based UndeRstandinG of gene clustERs☆15Feb 6, 2026Updated 3 months ago
- Taxonomic classification of DNA sequences☆57Jul 2, 2024Updated last year
- personal genome constructor☆11May 29, 2025Updated 11 months ago
- Computational Optimization of DNA Activity (CODA)☆68Apr 3, 2025Updated last year
- This repository contains the implementation of a novel machine learning classifier trained on the Dataset of Congruent Inhibitors and Dec…☆22Sep 8, 2020Updated 5 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- NRPSpredictor2 is a program to predict the specificity of bacterial and fungal adenylation domains.☆11Oct 7, 2019Updated 6 years ago
- Dynamic programming for aa-to-nt alignment with affine gap, splicing and frameshift☆19Sep 30, 2024Updated last year
- pandasGWAS: a Python package for easy retrieval of GWAS Catalog data☆17Dec 19, 2025Updated 5 months ago
- ☆13May 16, 2016Updated 10 years ago
- Multi-label subcellular localization and sorting signal prediction based on protein foundation models☆25Jan 12, 2026Updated 4 months ago
- This is a basic repository with all the scripts necessary to reconstruct the data analysis from our work on the 200 Genomes☆12Aug 31, 2018Updated 7 years ago
- Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities☆35May 24, 2024Updated 2 years ago