Chromatin interaction aware gene regulatory modeling with graph attention networks
☆28Feb 21, 2023Updated 3 years ago
Alternatives and similar repositories for GraphReg
Users that are interested in GraphReg are comparing it to the libraries listed below
Sorting:
- ENNGene: an Easy Neural Network model building tool for Genomics☆11Mar 31, 2022Updated 3 years ago
- Toolset for training quantitative sequence to function models.☆23Mar 15, 2024Updated last year
- scover☆24Nov 3, 2023Updated 2 years ago
- A lightweight reimplementation of some of the algorithms in the MEME suite in Python.☆28Feb 22, 2026Updated last week
- Machine learning methods for DNA sequence analysis.☆59Updated this week
- A method for analyzing scATAC-seq experiments.☆34Jun 20, 2025Updated 8 months ago
- Phasing of dikaryotic fungal genome assemblies☆13Mar 1, 2023Updated 3 years ago
- ☆26Nov 7, 2023Updated 2 years ago
- ☆21Dec 10, 2025Updated 2 months ago
- Blazing fast toolkit to work with .hic and .cool files☆42Feb 23, 2026Updated last week
- ☆21Jan 1, 2022Updated 4 years ago
- TF MOtif Discovery from Importance SCOres☆168Feb 20, 2026Updated last week
- ☆16Jan 14, 2026Updated last month
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Variational Auto Encoders for learning binding signatures of transcription factors☆14Mar 14, 2024Updated last year
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Jan 11, 2025Updated last year
- R functions for very fast eigenvector calculation☆11Jan 18, 2023Updated 3 years ago
- Importing and manipulating Hi-C data in R☆11Jul 17, 2025Updated 7 months ago
- PULSAR: a Foundation Model for Multi-scale and Multicellular Biology☆28Updated this week
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆13Oct 1, 2025Updated 5 months ago
- deepBreaks , a computational method, aims to identify important changes in association with the phenotype of interest using multi-alignme…☆12Oct 22, 2025Updated 4 months ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 4 months ago
- A useful tool for shuffling biological sequences while preserving the k-let counts☆14Apr 23, 2024Updated last year
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated last year
- A framework to score and analyze variant effects genome-wide using ChromBPNet models☆16Aug 1, 2025Updated 7 months ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 8 months ago
- Pipeline for Universal Mapping of ATAC-seq☆25Sep 23, 2025Updated 5 months ago
- Fully convolutional deep learning variant effect predictor architecture☆23Jan 3, 2024Updated 2 years ago
- Nextflow pipeline to re-process all public single-cell RNA-seq data☆31Jul 9, 2025Updated 7 months ago
- Species-aware DNA language models capture regulatory elements and their evolution☆28Aug 21, 2023Updated 2 years ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Apr 1, 2025Updated 11 months ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆100Sep 9, 2025Updated 5 months ago
- fastest GTF/GFF-to-BED converter chilling around☆32Jan 20, 2026Updated last month
- Formats Roary output for viewing in FriPan☆11May 23, 2018Updated 7 years ago
- ☆10Dec 11, 2024Updated last year
- ☆13Apr 7, 2023Updated 2 years ago
- A list of awesome bioinformatics communities☆19Oct 3, 2024Updated last year
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆16Jan 12, 2026Updated last month
- Analyzing Hi-C data in R with HiCExperiment objects☆15Mar 18, 2025Updated 11 months ago