Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of regulatory elements.
☆39Mar 27, 2025Updated 11 months ago
Alternatives and similar repositories for polygraph
Users that are interested in polygraph are comparing it to the libraries listed below
Sorting:
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Nov 15, 2024Updated last year
- Sequencing analysis pipeline☆15Dec 12, 2025Updated 2 months ago
- ENNGene: an Easy Neural Network model building tool for Genomics☆11Mar 31, 2022Updated 3 years ago
- Machine learning methods for DNA sequence analysis.☆57Feb 2, 2026Updated 3 weeks ago
- ☆24Jun 5, 2025Updated 8 months ago
- Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.☆50Oct 4, 2024Updated last year
- gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.☆317Updated this week
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆63Feb 5, 2026Updated 3 weeks ago
- Snakemake workflow for comparing E-G links to experimental data☆23Jan 22, 2026Updated last month
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆97Nov 13, 2025Updated 3 months ago
- ☆86Sep 20, 2023Updated 2 years ago
- Evaluating genomic sequence models for explaining personalized expression variation☆20Dec 6, 2023Updated 2 years ago
- ☆40Sep 17, 2024Updated last year
- Biological sequence analysis for the modern age.☆263Updated this week
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- NEFF Calculator and MSA File Converter☆13Sep 16, 2025Updated 5 months ago
- A flexible and fast sgRNA counter from FASTQ Files☆11Dec 29, 2025Updated 2 months ago
- ☆44Feb 11, 2026Updated 2 weeks ago
- Benchmarking DNA Language Models on Biologically Meaningful Tasks☆129Oct 31, 2024Updated last year
- Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"☆24Jun 26, 2024Updated last year
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Dec 2, 2024Updated last year
- pangenome from maximal blocks in an MSA☆11Sep 17, 2024Updated last year
- Python package for analyzing and visualizing iModulons☆14Jan 19, 2026Updated last month
- ☆13Jan 23, 2025Updated last year
- Genomic sequence preprocessing toolkit☆13Jan 13, 2026Updated last month
- ☆12Apr 8, 2021Updated 4 years ago
- ☆16Feb 15, 2026Updated last week
- De novo genome assembler.☆11Jul 30, 2018Updated 7 years ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆28Feb 21, 2023Updated 3 years ago
- A curated list of awesome resources, papers, datasets, and tools related to Genomic LLMs. This repository aims to provide a comprehensive…☆17Aug 7, 2024Updated last year
- A package for making MuE observation models in Edward2.☆13Jun 10, 2021Updated 4 years ago
- A port of biocommons/hgvs to the Rust programming language☆16Jan 30, 2026Updated last month
- ☆32Updated this week
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆55Nov 1, 2025Updated 3 months ago
- A better, faster way to count guides in CRISPR screens.☆34Apr 11, 2025Updated 10 months ago
- DeepMP is a computational tool to detect DNA modifications in Nanopore sequencing data☆28Mar 18, 2022Updated 3 years ago
- Matplotlib style for scientific publications☆14Updated this week
- An improved method for predicting toxicity of proteins☆18Aug 26, 2023Updated 2 years ago
- ☆14Feb 19, 2026Updated last week