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

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

Genome modeling and design across all domains of life

AcadHomepage: A Modern and Responsive Academic Personal Homepage

An extensible python-based genomics visualization engine

SMAC: Single Molecule 6mA analysis tool of CCS reads

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

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

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

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

R package detecting DNA modifications by kinetic data of SMRT sequencing

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

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

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

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…

A Python library for reading and writing PacBio® data files

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

Tools for fiberseq data written in rust.

A bioinformatics tool for working with modified bases

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

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

Nanomotif - a tool for identifying methylated motifs in metagenomic samples

The DevNet project on github stores the PacBio DevNet website.

Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics

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

AlphaFold2 non-docker setup

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

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

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

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