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SMALR: a framework for single-molecule level interrogation of the methylation status of SMRT reads.

Python 9 6 Updated Apr 12, 2018

An R package for de novo discovery of enriched DNA motifs (e.g. TFBS)

R 7 2 Updated May 28, 2019

Genome modeling and design across all domains of life

Jupyter Notebook 2,347 215 Updated Feb 24, 2025

AcadHomepage: A Modern and Responsive Academic Personal Homepage

SCSS 1,727 3,411 Updated Mar 3, 2025

An extensible python-based genomics visualization engine

Python 144 20 Updated Aug 11, 2023

SMAC: Single Molecule 6mA analysis tool of CCS reads

Raku 2 Updated Mar 3, 2025

A collection of softwares to handle and model PacBio kinetic signal data and predict epigenetics modifications.

C++ 10 1 Updated Mar 4, 2024

Retro-ingineering of PacBio's modelling of IPD (RSII, Sequel I, Sequel II v2)

Python 2 Updated Jan 30, 2024

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

Python 140,560 28,182 Updated Mar 4, 2025

DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models

Python 89 21 Updated Feb 6, 2025

R package detecting DNA modifications by kinetic data of SMRT sequencing

C++ 8 3 Updated Jul 31, 2014

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

Shell 340 81 Updated Dec 14, 2024

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Python 632 164 Updated Mar 9, 2024

Implement a ChatGPT-like LLM in PyTorch from scratch, step by step

Jupyter Notebook 41,321 5,574 Updated Mar 2, 2025

Accurate Typing of Diverse Immune-Related Gene Families from Long-Read Sequencing Data. It can handle HLA, KIR, IG, TCR, CYP gene families. It supports both WGS and amplicon data. It supports PacBi…

F* 8 Updated Feb 10, 2025

A Python library for reading and writing PacBio® data files

Python 39 27 Updated Feb 22, 2025

Scripts, notebooks, and methods for the SAMOSA-ChAAT SNF2h study from the Ramani & Narlikar labs

Jupyter Notebook 6 1 Updated Jan 19, 2022

Tools for fiberseq data written in rust.

Rust 44 6 Updated Feb 17, 2025

A bioinformatics tool for working with modified bases

Rust 174 8 Updated Feb 27, 2025

Contains codes for the meta-analysis investigating sex differences in mice gut microbiome variability

R 1 Updated Mar 4, 2025

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing

Python 45 1 Updated Jan 23, 2025

Nanomotif - a tool for identifying methylated motifs in metagenomic samples

Python 25 1 Updated Feb 28, 2025

The DevNet project on github stores the PacBio DevNet website.

116 29 Updated Jul 9, 2018

Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics

HTML 183 35 Updated Feb 12, 2025

Repository for "Comparison of long read sequencing technologies in interrogating bacteria and fly genomes"

7 Updated Mar 15, 2021

AlphaFold2 non-docker setup

Shell 351 121 Updated Nov 24, 2023

nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nanopore sequencing.

R 68 7 Updated May 20, 2022

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

262 45 Updated Feb 4, 2025

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Python 233 36 Updated Oct 9, 2024

Tools for detecting DNA modifications from single molecule, real-time sequencing data

Python 22 22 Updated Feb 24, 2022
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