Rna Python Packages

seqfold

nucleic acid folding

helical

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

graphein

Protein Graph Library

rnaglib

RNAglib: Tools for learning on the structure of RNA using 2.5D geometric representations

eltetrado

Find and classify tetrads and quadruplexes in DNA/RNA 3D structure

squarna

RNA secondary structure prediction tool

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

pipeclip

PIPELINE FOR CLIP SEQ DATA

ncrnabert

ncRNABert: Deciphering the landscape of non-coding RNA using language model

chilife

Python package for site-directed spin labeling of proteins

pyaragorn

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

metagene

Metagene Profiling Analysis and Visualization

streq

🧬 Python utilities for working with nucleotide sequence strings.

deeprm

Deep learning for RNA Modification

hunana

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

rnpfind

Bioinformatics tool for exploring RNA-Protein interactions

seqme

Metrics for evaluating biological sequence design

bpforms

Unambiguous representation of modified DNA, RNA, and proteins

pytximport

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

unitvelo

Temporally unified RNA velocity inference

dashingturtle

An application for building structural landscapes of RNA sequence modifications with Nanopore data. 📘 Documentation: https://dashing-turtle.readthedocs.io/

ga4gh

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

starseqr

RNA Fusion Detection and Quantification

xpore

xpore is a python package for Nanopore data analysis of differential RNA modifications.