deep learning-inspired explainable sequence model for transcription initiation
☆102Mar 3, 2025Updated last year
Alternatives and similar repositories for puffin
Users that are interested in puffin are comparing it to the libraries listed below
Sorting:
- ☆18Oct 21, 2024Updated last year
- RNA-seq prediction with deep convolutional neural networks.☆227Aug 28, 2025Updated 6 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 4 months ago
- A lightweight reimplementation of some of the algorithms in the MEME suite in Python.☆28Feb 22, 2026Updated last week
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆97Nov 13, 2025Updated 3 months ago
- COsine SImilarity-based Genotyper using pangenomes☆31Feb 13, 2026Updated 3 weeks ago
- Scoring GT/AG sites for improving spliced alignment☆51Nov 10, 2025Updated 3 months ago
- Machine learning methods for DNA sequence analysis.☆59Feb 27, 2026Updated last week
- accurate prediction of promoter activity and variant effects from massive parallel reporter assays☆43Jul 3, 2025Updated 8 months ago
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 4 months ago
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆13Oct 1, 2025Updated 5 months ago
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆317Updated this week
- ☆27Apr 15, 2025Updated 10 months ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆96Mar 1, 2025Updated last year
- Biological sequence analysis for the modern age.☆263Feb 22, 2026Updated last week
- ☆21Dec 13, 2024Updated last year
- An accurate aligner of long reads to a variation graph, based on co-linear chaining☆35May 23, 2025Updated 9 months ago
- TF MOtif Discovery from Importance SCOres☆168Feb 20, 2026Updated 2 weeks ago
- Interspecies Point Projection - A tool for comparative genomics beyond alignable sequence☆24Feb 9, 2026Updated 3 weeks ago
- ANI based satellite annotation☆23Nov 7, 2025Updated 4 months ago
- Sequential regulatory activity predictions with deep convolutional neural networks.☆466Jan 15, 2026Updated last month
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Oct 4, 2024Updated last year
- Unzip assembly graphs with Hi-C data and/or long reads.☆27Sep 20, 2024Updated last year
- Methylation analysis pipeline for genome graph☆15May 25, 2025Updated 9 months ago
- An R package for comparative transcriptomic analyses of hybrids and their progenitors☆15Sep 5, 2024Updated last year
- This repository hosts a minimal version of a Python API for BPNet.☆55Jan 24, 2026Updated last month
- Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/☆290Jun 16, 2025Updated 8 months ago
- Fast alignment and preprocessing of chromatin profiles☆214Jan 17, 2026Updated last month
- ☆16Mar 17, 2023Updated 2 years ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆87Sep 24, 2025Updated 5 months ago
- Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)☆211Feb 2, 2026Updated last month
- Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them☆175Oct 10, 2025Updated 4 months ago
- a framework for training sequence-level deep learning networks☆399Dec 16, 2024Updated last year
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 6 months ago
- ☆15Jun 29, 2021Updated 4 years ago
- A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution☆14Feb 24, 2026Updated last week
- The IntroBlocker ancestry inference algorithm☆17Oct 24, 2023Updated 2 years ago
- Genomic Pre-trained Network☆325Feb 24, 2026Updated last week