A method to predict DNA shape features considering farther flanking region.
☆41Sep 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☆80Mar 19, 2025Updated last year
- Interpretable bimodal network for transcription factors binding site prediction☆10Jun 29, 2023Updated 3 years ago
- ☆10Jan 19, 2019Updated 7 years ago
- 📦 A Command Line Tool for downloading protein structures, sequences and MSAs☆10Nov 21, 2017Updated 8 years ago
- ☆36Jan 27, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Recurrent Variational Auto gene encoder☆19Jan 12, 2023Updated 3 years ago
- R package for high-throughput DNA shape predictions and feature encoding☆20Jul 1, 2021Updated 5 years ago
- ☆13Apr 7, 2023Updated 3 years ago
- A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and buildin…☆27Jul 15, 2025Updated last year
- RoseTTAFold2 protein/nucleic acid complex prediction☆379Jun 3, 2024Updated 2 years 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
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆14Oct 16, 2025Updated 9 months ago
- A Xojo/python tool for identification and annotation of transcription factor binding sites in bacterial genomes☆19Updated this week
- Pipeline for eukaryotic genome annotation based on external evidences☆15Feb 23, 2023Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆13Jan 23, 2025Updated last year
- code to run sei and obtain sei and sequence class predictions☆115Dec 20, 2022Updated 3 years ago
- fastest GTF/GFF-to-BED converter chilling around☆32Jun 16, 2026Updated last month
- ☆21Mar 20, 2017Updated 9 years ago
- PhenomeXcan: mapping the genome to the phenome through the transcriptome☆11Jun 28, 2020Updated 6 years ago
- ☆15Nov 11, 2019Updated 6 years ago
- An introductory workshop to protein language models☆17May 24, 2022Updated 4 years ago
- ☆10Dec 12, 2017Updated 8 years ago
- ☆12Feb 6, 2023Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- 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
- 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
- Computational Optimization of DNA Activity (CODA)☆69Apr 3, 2025Updated last year
- HMmer Based UndeRstandinG of gene clustERs☆15Feb 6, 2026Updated 6 months ago
- personal genome constructor☆11May 29, 2025Updated last year
- NRPSpredictor2 is a program to predict the specificity of bacterial and fungal adenylation domains.☆12Oct 7, 2019Updated 6 years ago
- Python package to run DefensePredictor, a machine learning model to identify proteins involved in anti-phage defense☆56Apr 27, 2026Updated 3 months ago
- Taxonomic classification of DNA sequences☆57Jul 2, 2024Updated 2 years ago
- ☆13May 16, 2016Updated 10 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.☆19Feb 15, 2026Updated 5 months ago
- Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities☆36May 24, 2024Updated 2 years ago
- CliXO algorithm re-implemented☆16Nov 9, 2021Updated 4 years ago
- Software to study why most genes are ignored☆15Sep 18, 2018Updated 7 years ago
- S3norm ver2 + IDEAS epigenetic state / master peak list☆12Sep 22, 2023Updated 2 years ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆44Jul 3, 2025Updated last year
- Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.☆18Jan 14, 2025Updated last year