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    57 repositories

    • ribiosNGS

      Public
      Next-generation sequencing data analysis with ribios
      R
      •2•2•5•0•Updated May 1, 2026May 1, 2026

    • besca

      Public
      BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
      Python
      •
      GNU General Public License v3.0
      •17•50•32•4•Updated Apr 8, 2026Apr 8, 2026

    • besca_publication_results

      Public
      Jupyter Notebook
      •1•4•0•0•Updated Apr 7, 2026Apr 7, 2026

    • ribiosGSEA

      Public
      Functions for gene-set analysis of various kinds supported by ribios
      R
      •2•2•3•0•Updated Mar 28, 2026Mar 28, 2026

    • designit

      Public
      Blocking and randomization for experimental design
      randomizationrstatsdesign-of-experiments
      randomizationrstatsdesign-of-experiments
      HTML
      •
      Other
      •1•8•15•4•Updated Mar 27, 2026Mar 27, 2026

    • ribiosUtils

      Public
      The ribiosUtils package, a swiss-army knife for bioinformatics and computational biology tasks in drug discovery
      C
      •1•1•0•0•Updated Mar 17, 2026Mar 17, 2026

    • ribiosMath

      Public
      Mathematical objects and functions in the ribios software suite
      R
      •2•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • ribiosPlot

      Public
      Data transformation and visualization with the ribios suite
      R
      •1•1•0•0•Updated Feb 20, 2026Feb 20, 2026

    • ribios

      Public
      ribios: R interface to BIOS - a suite of R packages for computational biology
      R
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • FAPLTBRpreclinical_ST_publication

      Public
      Notebooks used to produce results for spatial transcriptomics analysis presented in the publication "FAP-Targeted LTBR Agonist Drives HEV Differentiation and Im…
      Jupyter Notebook
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • ribiosExpression

      Public
      Data structure and functions for gene expression analysis
      R
      •1•0•1•0•Updated Feb 18, 2026Feb 18, 2026

    • bedapub.r-universe.dev

      Public
      For R packages that are listed in r-universe.de
      0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • ribiosArg

      Public
      ribiosArg handles arguments for command-line, stand-alone R programs
      R
      •1•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • ribiosGraph

      Public
      Tools to manipulate and visualize graph objects in the 'ribios' software suite
      R
      •1•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • ribiosIO

      Public
      File input and output module of the ribios suite
      C
      •1•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • sr-domain

      Public
      Pipeline for extracting structured toxicology findings from preclinical study reports using LLMs with controlled generation. Converts PDF reports to markdown, e…
      Python
      •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • ribiosAnnotation

      Public
      Annotate features (genes, mRNAs, proteins, ...) with ribios
      R
      •1•0•2•0•Updated Feb 15, 2026Feb 15, 2026

    • dynamic-form

      Public
      Python
      •
      GNU General Public License v3.0
      •0•2•0•1•Updated Jan 9, 2026Jan 9, 2026

    • 2025-10-Zukunftstag-simulation

      Public
      Für Roche's Zukunftstag 2025
      Jupyter Notebook
      •1•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • splicekit

      Public
      splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
      Python
      •
      GNU General Public License v3.0
      •4•23•5•0•Updated Nov 28, 2025Nov 28, 2025

    • bksnake

      Public
      Public version of bksnake - biokit snakemake - bulk RNASeq Snakemake workflow
      Python
      •0•2•0•0•Updated Nov 7, 2025Nov 7, 2025

    • fm_Fg_prediction

      Public
      R
      •0•0•0•0•Updated Sep 22, 2025Sep 22, 2025

    • tobemstomig_in_vivo_TILs_Panc02_publication

      Public
      Single cell RNA-seq of Panc02-H7-Fluc model with vehicle, tobemstomig, nivolumab and relatlimab-like treatment
      Jupyter Notebook
      •0•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • PMDA-Summer-School

      Public
      Public website of Roche PMDA Summer School
      GNU General Public License v3.0
      •3•4•0•0•Updated May 21, 2025May 21, 2025

    • TCBinducedTMEreprogramming_CEATCBMC38_scRNAseq_publication-

      Public
      Notebooks used to produce results for the publication "Tumor Microenvironment Reprogramming Induced by T Cell Engager Treatment" related to the in vivo CEA-TCB …
      Jupyter Notebook
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • AAVimmuneresponse_scRNAseq_PBMC_publication

      Public
      Notebooks utilized to produce results for the publication "Innate immune response to AAV-based gene therapy vectors: mechanisms of complement activation and cyt…
      Jupyter Notebook
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • kinex

      Public
      Kinex infers causal kinases from phosphoproteomics data
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Dec 8, 2024Dec 8, 2024

    • ComplexSim

      Public
      R
      •0•1•0•0•Updated Sep 20, 2024Sep 20, 2024

    • HBVouroboros

      Public
      HBVouroboros automates sequencing-based HBV genotyping and expression profiling
      bioinformaticssnakemakeexpression
      bioinformaticssnakemakeexpressionhbvgenotypingsnakemake-workflow
      Python
      •
      GNU General Public License v3.0
      •2•3•5•6•Updated Jul 9, 2024Jul 9, 2024

    • ribiosScripts

      Public
      Rscripts as command-line tools from the corresponding repository on BEDA github.
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 17, 2024Jun 17, 2024
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