Rna Python Packages

coralsnake

Exon-aware RNA pipeline: splicing-aware liftover (tbam2gbam/gbam2tbam), metagene, annotation

seqfold

nucleic acid folding

rna-tools

🔧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

graphein

Protein Graph Library

helical

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

sirna-data-grabber

A Python loader for 18k+ siRNA knockdown-efficacy records across 10 sources, each source has its own license.

rnaglib

Toolkit for structure-based deep learning on RNA.

proteinmotion

Animate proteins, DNA, and RNA in Python with a Manim-inspired API, native GPU rendering, and Blender EEVEE.

eltetrado

A Python application to find and classify tetrads and quadruplexes in DNA/RNA 3D structures

minerva-dna

Coevolutionary discovery using genome language models

pyaragorn

Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.

adabmdca

Pytorch implementation of adabmDCA

pytximport

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

metagene

Metagene Profiling Analysis and Visualization

squarna

RNA secondary structure prediction tool

risearch

Blazing fast search for RNA and DNA hybridization with nearest-neighbour thermodynamics

seqme

Metrics for evaluating biological sequence design

chilife

Python package for site-directed spin labeling of proteins

rnpfind

Bioinformatics tool for exploring RNA-Protein interactions

barnaba

Analyse Nucleic Acids Structure and Simulations with baRNAba

deeprm

Deep learning for RNA Modification

bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

hunana

A command-line tool that analyses the diversity and motifs of protein/nucleotide sequences.

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)