A method to predict DNA shape features considering farther flanking region.
☆39Sep 25, 2024Updated last year
Alternatives and similar repositories for deepDNAshape
Users that are interested in deepDNAshape are comparing it to the libraries listed below
Sorting:
- Geometric deep learning of protein–DNA binding specificity☆76Mar 19, 2025Updated 11 months ago
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆12Oct 16, 2025Updated 4 months ago
- ☆10Jan 19, 2019Updated 7 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
- Pipeline for eukaryotic genome annotation based on external evidences☆14Feb 23, 2023Updated 3 years ago
- PhenomeXcan: mapping the genome to the phenome through the transcriptome☆11Jun 28, 2020Updated 5 years ago
- Interpretable bimodal network for transcription factors binding site prediction☆10Jun 29, 2023Updated 2 years ago
- fastest GTF/GFF-to-BED converter chilling around☆32Jan 20, 2026Updated last month
- ☆13May 16, 2016Updated 9 years ago
- ☆11Feb 6, 2023Updated 3 years ago
- ☆13Apr 7, 2023Updated 2 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
- Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)☆12May 22, 2025Updated 9 months ago
- A collection of command-line tools I wrote to make various repetitive tasks more convenient☆16Jan 27, 2026Updated last month
- ☆34Jan 27, 2025Updated last year
- Software for linkage disequilibrium graphical models☆16Apr 6, 2025Updated 10 months ago
- ☆13Jul 5, 2019Updated 6 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
- pandasGWAS: a Python package for easy retrieval of GWAS Catalog data☆17Dec 19, 2025Updated 2 months ago
- Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.☆17Jan 14, 2025Updated last year
- A Xojo/python tool for identification and annotation of transcription factor binding sites in bacterial genomes☆19Jan 16, 2026Updated last month
- Scripts for population genetics analysis☆20Nov 10, 2022Updated 3 years ago
- Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021☆16Apr 8, 2021Updated 4 years ago
- Utilities for analyzing next generation sequencing data.☆15May 7, 2021Updated 4 years ago
- CliXO algorithm re-implemented☆16Nov 9, 2021Updated 4 years ago
- Python package to run DefensePredictor, a model that identifies proteins involved in anti-phage defense☆16Dec 17, 2025Updated 2 months ago
- HMmer Based UndeRstandinG of gene clustERs☆15Feb 6, 2026Updated 3 weeks ago
- Benchmarking gene and variant prioritization algorithms for GWAS data☆15Feb 27, 2020Updated 6 years ago
- An introductory workshop to protein language models☆17May 24, 2022Updated 3 years ago
- ☆21Mar 20, 2017Updated 8 years ago
- Repo to analyze population genetic data with many different methods☆15Oct 23, 2019Updated 6 years ago
- Leroy & Rougemont - “learning-by-doing” introduction to population genomics - scripts☆21Oct 2, 2019Updated 6 years ago
- code to run sei and obtain sei and sequence class predictions☆110Dec 20, 2022Updated 3 years ago
- Bioinformatics scripts for genome analysis☆17Oct 26, 2022Updated 3 years ago
- Multi-label subcellular localization and sorting signal prediction based on protein foundation models☆22Jan 12, 2026Updated last month
- Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.☆19Aug 28, 2025Updated 6 months ago
- RoseTTAFold2 protein/nucleic acid complex prediction☆375Jun 3, 2024Updated last year
- crussmap is a faster tool to convert genome coordinates between difference reference assemblies.☆21May 4, 2023Updated 2 years ago