Scientific Software
Updated 10 months ago

Nextclade — Peer-reviewed • Rank 14.3 • Science 95%

Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)

Updated 10 months ago

rna-tools • Rank 14.2 • Science 77%

🔧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

Updated 10 months ago

isoseq • Rank 4.6 • Science 77%

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

Updated 10 months ago

unitvelo • Rank 9.2 • Science 67%

UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference

Updated 10 months ago

hlatyping • Rank 7.2 • Science 67%

Precision HLA typing from next-generation sequencing data

Updated 10 months ago

nascent • Rank 7.2 • Science 67%

Nascent Transcription Processing Pipeline

Updated 10 months ago

rnafusion • Rank 8.4 • Science 57%

RNA-seq analysis pipeline for detection of gene-fusions

Updated 10 months ago

rnasplice • Rank 6.9 • Science 57%

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

Updated 10 months ago

Structstrings • Rank 12.8 • Science 49%

:package: Structstrings: implementation of Biostrings to work with dot bracket annotations

Updated 10 months ago

rnaseq • Rank 11.6 • Science 49%

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

Updated 10 months ago

https://github.com/althonos/pyaragorn • Rank 7.4 • Science 49%

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

Updated 10 months ago

pybarrnap • Rank 7.2 • Science 44%

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

Updated 10 months ago

RNAmodR.RiboMethSeq • Rank 9.9 • Science 39%

:package: RNAmodR.RiboMethSeq: detection of 2'-O methylations by RiboMethSeq

Updated 10 months ago

barnaba • Rank 10.8 • Science 33%

Analyse Nucleic Acids Structure and Simulations with baRNAba

Updated 10 months ago

aroma.affymetrix • Rank 12.5 • Science 23%

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

Updated 10 months ago

RNAmodR • Rank 12.1 • Science 23%

:package: RNAmodR: detection of post-transcriptional RNA modifications based on HTS data

Updated 10 months ago

ga4gh-server • Rank 11.9 • Science 10%

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

Updated 10 months ago

oncoanalyser • Science 57%

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Updated 10 months ago

acid • Science 26%

Generate the AutoCorrelation Integral Drill (ACID) test set with scripts and workflows for robust validation of autocorrelation algorithms. 🌐📊

Updated 10 months ago

desirna • Science 67%

State of the art software for RNA sequence design. The first to solve the Eterna benchmark!

Updated 10 months ago

fingernat-ml • Science 49%

Data accompanying the manuscript on SIFts- and ML-based methods in Virtual Screening for RNA binding ligands.

Updated 10 months ago

rna-ligand-based • Science 49%

Evaluation of ligand based methods applied to RNA and DNA targets

Updated 10 months ago

SimpleBio • Science 54%

Easy-to-use biological sequence tools working with DNA, RNA and aminoacid sequences.

Updated 10 months ago

https://github.com/marcom/plotrna.jl • Science 26%

Plot nucleic acid secondary structures with Julia

Updated 10 months ago

rnaswarm • Science 44%

RNAswarm is a nextflow pipeline for differential RNA-RNA interaction analysis using RNA cross-linking methodologies

Updated 10 months ago

pytximport • Science 39%

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