Identification of differential RNA modifications from nanopore direct RNA sequencing

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

RiboNucleic Acid (RNA) Language Model

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

nucleic acid folding

Visualise RNA secondary structure in consistent, reproducible and recognisable layouts

Nucleic Acids Research 2024：RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention map to match different types of downstream tasks.

Recurrent Neural Aligner

Toolkit for structure-based deep learning on RNA.

Primary RNA sequence model

Feature-rich Python implementation of the tximport package for gene count estimation.

🧪 Ultrafast bisulfite

A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence

RNAcentral website source code

Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

Pipeline for de novo clustering of long transcriptomic reads

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Clair3-RNA - a long-read small variant caller for RNA sequencing data

TransfoRNA: Navigating the Uncertainties of Small RNA Annotation with an Adaptive Machine Learning Strategy

Python implementation of barrnap (Bacterial ribosomal RNA predictor)