RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Protein Graph Library

a JavaScript DNA, RNA, and protein sequence viewer

gRNAde is a Generative AI framework for inverse design of 3D RNA structure and function

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

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

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...

RNA-seq analysis pipeline for detection of gene-fusions

Identification of differential RNA modifications from nanopore direct RNA sequencing

RiboNucleic Acid (RNA) Language Model

A high-performance, pure Rust toolkit for standardizing and preparing biomolecular systems (proteins & nucleic acids). It heals missing atoms, resolves protonation states, adds solvation, and unifies topologies to forge simulation-ready structures.

:microscope::books: Galaxy Tool wrappers

nucleic acid folding

RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.

A comprehensive cancer DNA/RNA analysis and reporting pipeline

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

ABRA2

Visualise RNA secondary structure in consistent, reproducible and recognisable layouts

A course on genomics and bioinformatics from WashU

Precision HLA typing from next-generation sequencing data

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.

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

A high-performance modification detection tool in Rust

gatk4 RNA variant calling pipeline

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

Recurrent Neural Aligner

Efficient target prediction incorporating accessibility of interaction sites