Nextclade
Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)
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
unitvelo
UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference
Structstrings
:package: Structstrings: implementation of Biostrings to work with dot bracket annotations
https://github.com/althonos/pyaragorn
Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.
pybarrnap
Python implementation of barrnap (Bacterial ribosomal RNA predictor)
RNAmodR.RiboMethSeq
:package: RNAmodR.RiboMethSeq: detection of 2'-O methylations by RiboMethSeq
aroma.affymetrix
🔬 R package: Analysis of Large Affymetrix Microarray Data Sets
RNAmodR
:package: RNAmodR: detection of post-transcriptional RNA modifications based on HTS data
ga4gh-server
Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
acid
Generate the AutoCorrelation Integral Drill (ACID) test set with scripts and workflows for robust validation of autocorrelation algorithms. 🌐📊
desirna
State of the art software for RNA sequence design. The first to solve the Eterna benchmark!
fingernat-ml
Data accompanying the manuscript on SIFts- and ML-based methods in Virtual Screening for RNA binding ligands.
helical
A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.
rna-ligand-based
Evaluation of ligand based methods applied to RNA and DNA targets
SimpleBio
Easy-to-use biological sequence tools working with DNA, RNA and aminoacid sequences.
https://github.com/marcom/plotrna.jl
Plot nucleic acid secondary structures with Julia
rnaswarm
RNAswarm is a nextflow pipeline for differential RNA-RNA interaction analysis using RNA cross-linking methodologies
pytximport
Feature-rich Python implementation of the tximport package for gene count estimation.