deep learning-inspired explainable sequence model for transcription initiation
☆106Mar 3, 2025Updated last year
Alternatives and similar repositories for puffin
Users that are interested in puffin are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆19Oct 21, 2024Updated last year
- RNA-seq prediction with deep convolutional neural networks.☆256Aug 28, 2025Updated 10 months ago
- 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
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 8 months ago
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆44Jul 3, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Machine learning methods for DNA sequence analysis.☆64Jul 20, 2026Updated last week
- Biological sequence analysis for the modern age.☆305Jul 19, 2026Updated last week
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆334Jun 12, 2026Updated last month
- ☆27Apr 15, 2025Updated last year
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆98Jun 10, 2026Updated last month
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆102Mar 1, 2025Updated last year
- TF MOtif Discovery from Importance SCOres☆188May 13, 2026Updated 2 months ago
- a framework for training sequence-level deep learning networks☆403Dec 16, 2024Updated last year
- This repository hosts a minimal version of a Python API for BPNet.☆60Jul 19, 2026Updated last week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Sequential regulatory activity predictions with deep convolutional neural networks.☆473Jan 15, 2026Updated 6 months ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆240Jun 9, 2026Updated last month
- ☆21Dec 13, 2024Updated last year
- Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them☆182Mar 19, 2026Updated 4 months ago
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆14Apr 28, 2026Updated 2 months ago
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 8 months ago
- GFA visualization tool - Rust reimplementation of odgi viz☆15May 2, 2026Updated 2 months ago
- An accurate aligner of long reads to a variation graph, based on co-linear chaining☆35May 23, 2025Updated last year
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆92Sep 24, 2025Updated 10 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Scoring GT/AG sites for improving spliced alignment☆58Nov 10, 2025Updated 8 months ago
- Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/☆288Jun 16, 2025Updated last year
- Genomic Pre-trained Network☆349Updated this week
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆52Oct 4, 2024Updated last year
- A lightweight reimplementation of some of the algorithms in the MEME suite in Python.☆33Jun 3, 2026Updated last month
- ☆17Mar 17, 2023Updated 3 years ago
- Fast alignment and preprocessing of chromatin profiles☆225Mar 20, 2026Updated 4 months ago
- Deep learning models to predict enhancers in different Drosophila embryo tissues☆20Dec 10, 2023Updated 2 years ago
- ☆10Jan 27, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution☆15Jul 14, 2026Updated last week
- [ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome☆507Jan 1, 2026Updated 6 months ago
- Code used to analyze single cell RNA and ATAC sequencing in developing human brain☆36Jan 4, 2022Updated 4 years ago
- Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)☆264Mar 24, 2026Updated 4 months ago
- a precise pangenome browser combining linear and graph-based pan-genome☆13Jul 16, 2024Updated 2 years ago
- Evaluating genomic sequence models for explaining personalized expression variation☆20Dec 6, 2023Updated 2 years ago
- scover☆23Nov 3, 2023Updated 2 years ago