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@rnajena RNA Bioinformatics and High-Throughput Analysis Jena

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    23 repositories

    • sugar

      Public
      S*R -- A Python framework for bioinformatics
      Python
      •0•2•0•0•Updated Feb 19, 2025Feb 19, 2025

    • dynamont

      Public
      C++
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Feb 18, 2025Feb 18, 2025

    • anchorna

      Public
      Find anchors in RNA/DNA sequences
      Python
      •0•2•0•0•Updated Feb 14, 2025Feb 14, 2025

    • viralclust

      Public
      Small pipeline to cluster viral genomes based on their k-mer content. WiP
      Nextflow
      •
      GNU General Public License v3.0
      •5•16•7•0•Updated Feb 6, 2025Feb 6, 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•2•2•0•Updated Jan 3, 2025Jan 3, 2025

    • diffONT

      Public
      diffONT is a python-based tool for predicting methylation-specific PCR (MSP) primers, based on Nanopore sequencing data. Given mutliple bedmethyl files, diffONT detects methylation specific PCR primer regions, which can distinguish between two groups of samples (originally cancer patients vs. healthy controls).
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • read5_ont

      Public
      Wrapper to read fast5 and pod5 files.
      raw-dataoxford-nanoporefast5ontoxford-nanopore-datapod5
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • read5

      Public
      Wrapper to read fast5, slow5, blow5 and pod5 files.
      raw-dataoxford-nanoporefast5ontoxford-nanopore-datapod5blow5slow5
      Python
      •
      GNU General Public License v3.0
      •1•9•1•0•Updated Nov 27, 2024Nov 27, 2024

    • poseidon

      Public
      PoSeiDon: positive selection detection and recombination analysis pipeline
      C
      •
      MIT License
      •9•36•9•0•Updated Oct 28, 2024Oct 28, 2024

    • 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 tool also includes features like read count normalization, filtering read counts by gene annotation and various visualization options.
      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
      •8•50•5•0•Updated Jul 2, 2024Jul 2, 2024

    • bertax_training

      Public
      Training scripts for BERTax
      Python
      •5•9•1•0•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

    • magnipore

      Public
      Magnipore: Differential single nucleotide changes of ONT signals
      oxford-nanoporecomparative-analysisepigenomicsepitranscriptomicsontraw-signal
      Red
      •
      GNU General Public License v3.0
      •0•5•0•0•Updated Mar 4, 2024Mar 4, 2024

    • vidhop

      Public
      VIDHOP is a virus host predicting tool. Its able to predict influenza A virus, rabies lyssavirus and rotavirus A.
      Python
      •8•19•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
      •6•16•0•0•Updated Sep 7, 2022Sep 7, 2022

    • vegeta

      Public
      work in progress
      Python
      •
      GNU General Public License v3.0
      •2•4•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