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@rnajena RNA Bioinformatics and High-Throughput Analysis Jena

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    28 repositories

    • sugar

      Public
      S*R -- A Python framework for bioinformatics
      Python
      •
      MIT License
      •1•6•0•0•Updated Feb 16, 2026Feb 16, 2026

    • SweetSynteny

      Public
      Python
      •
      MIT License
      •1•2•0•0•Updated Feb 6, 2026Feb 6, 2026

    • viralclust

      Public
      Small pipeline to cluster viral genomes based on their k-mer content. WiP
      Nextflow
      •
      GNU General Public License v3.0
      •5•17•7•0•Updated Feb 3, 2026Feb 3, 2026

    • dynamont

      Public
      hmmnanoporecppsignal-processingpython3ontnanopore-sequencingforward-backward-algorithm
      C++
      •
      GNU General Public License v3.0
      •1•5•0•1•Updated Jan 12, 2026Jan 12, 2026

    • diffMONT

      Public
      diffMONT is a python-based tool for predicting methylation-specific PCR (MSP) primers, based on Nanopore sequencing data. Given mutliple bedmethyl files, diffMO…
      Python
      •
      MIT License
      •0•3•0•0•Updated Nov 18, 2025Nov 18, 2025

    • DnaFeaturesViewerLite

      Public
      :eye: Python library to plot DNA sequence features (e.g. from Genbank files) -- lite version
      Python
      •
      MIT License
      •104•1•0•0•Updated Nov 12, 2025Nov 12, 2025

    • AssayBLAST

      Public
      Python
      •
      MIT License
      •0•4•1•0•Updated Oct 24, 2025Oct 24, 2025

    • RNAswarm

      Public
      RNAswarm is a nextflow pipeline for differential RNA-RNA interaction analysis using RNA cross-linking methodologies
      bioinformaticspipelinernarna-rna-interactionsrna-stucture-probing
      Python
      •
      MIT License
      •1•3•2•0•Updated Oct 16, 2025Oct 16, 2025

    • poseidon

      Public
      PoSeiDon: positive selection detection and recombination analysis pipeline
      C
      •
      MIT License
      •8•39•8•0•Updated Sep 22, 2025Sep 22, 2025

    • bayhunter

      Public
      BayHunter: A Bayesian approach to inferring the differential expression of small RNAs from read counts
      0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • anchorna

      Public
      Find anchors in RNA/DNA sequences
      Python
      •
      MIT License
      •0•6•0•0•Updated Aug 14, 2025Aug 14, 2025

    • anchorna_paper

      Public
      Code repository for the AnchoRNA publication
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 4, 2025Jul 4, 2025

    • magnipore

      Public
      Magnipore: Differential single nucleotide changes of ONT signals
      oxford-nanoporecomparative-analysisepigenomicsepitranscriptomicsontraw-signal
      Red
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated May 5, 2025May 5, 2025

    • read5_ont

      Public
      Wrapper to read fast5 and pod5 files.
      raw-dataoxford-nanoporefast5ontoxford-nanopore-datapod5
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Apr 5, 2025Apr 5, 2025

    • read5

      Public
      Wrapper to read fast5, slow5, blow5 and pod5 files.
      raw-dataoxford-nanoporefast5ontoxford-nanopore-datapod5blow5slow5
      Python
      •
      GNU General Public License v3.0
      •1•13•1•0•Updated Mar 26, 2025Mar 26, 2025

    • pcago-unified

      Public
      PCAGO is an interactive web service that allows analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. The to…
      R
      •3•1•1•0•Updated Sep 18, 2024Sep 18, 2024

    • bertax

      Public
      Taxonomic classification of DNA sequences
      Python
      •
      GNU General Public License v3.0
      •10•57•2•0•Updated Jul 2, 2024Jul 2, 2024

    • bertax_training

      Public
      Training scripts for BERTax
      Python
      •5•12•1•1•Updated Jun 12, 2024Jun 12, 2024

    • pcago

      Public
      Interactive web service that allows analysis of RNA-Seq read count data with PCA and clustering.
      R
      •
      GNU General Public License v3.0
      •0•0•5•0•Updated May 31, 2024May 31, 2024

    • pcago-electron

      Public
      Runs PCAGO as standalone desktop application using the Electron framework.
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 31, 2024May 31, 2024

    • Nanopore_Seq_Metaanalysis

      Public
      HTML
      •0•1•0•0•Updated Mar 7, 2024Mar 7, 2024

    • vidhop

      Public
      VIDHOP is a virus host predicting tool. Its able to predict influenza A virus, rabies lyssavirus and rotavirus A.
      Python
      •9•23•1•0•Updated May 7, 2023May 7, 2023

    • mycovista

      Public
      Mycovista - M. bovis assembly pipeline
      Python
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Mar 24, 2023Mar 24, 2023

    • EpiDope

      Public
      Prediction of B-cell epitopes from amino acid sequences using deep neural networks.
      Python
      •
      MIT License
      •7•18•0•0•Updated Sep 7, 2022Sep 7, 2022

    • vegeta

      Public
      work in progress
      Python
      •
      GNU General Public License v3.0
      •1•3•4•0•Updated Dec 17, 2021Dec 17, 2021

    • corfusi

      Public
      cORFusi - correction of ORFs utilizing short-read information
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 7, 2021Jun 7, 2021

    • epitop_pred

      Public
      scripts needed to generate a model which predicts epitops
      Python
      •
      Creative Commons Zero v1.0 Universal
      •2•2•1•0•Updated Nov 30, 2020Nov 30, 2020

    • bats_ncrna

      Public
      A comprehensive annotation of non-coding RNAs in available bat genome assemblies
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 30, 2019Apr 30, 2019