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    49 repositories

    • splicekit

      Public
      splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
      Python
      •
      GNU General Public License v3.0
      •4•15•3•0•Updated Jan 20, 2025Jan 20, 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 MC38-huCEA data.
      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 cytokine release"
      Jupyter Notebook
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • besca

      Public
      BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
      Python
      •
      GNU General Public License v3.0
      •17•49•30•7•Updated Jan 8, 2025Jan 8, 2025

    • bksnake

      Public
      Public version of bksnake - biokit snakemake - bulk RNASeq Snakemake workflow
      Python
      •0•2•0•0•Updated Dec 23, 2024Dec 23, 2024

    • 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

    • ribiosUtils

      Public
      The ribiosUtils package, a swiss-army knife for bioinformatics and computational biology tasks in drug discovery
      C
      •1•0•1•0•Updated Dec 5, 2024Dec 5, 2024

    • designit

      Public
      Blocking and randomization for experimental design
      randomizationrstatsdesign-of-experiments
      HTML
      •
      Other
      •1•8•15•3•Updated Nov 11, 2024Nov 11, 2024

    • ribiosIO

      Public
      File input and output module of the ribios suite
      C
      •1•0•0•0•Updated Oct 17, 2024Oct 17, 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
      bioinformaticssnakemakeexpressionhbvgenotypingsnakemake-workflow
      Python
      •
      GNU General Public License v3.0
      •1•2•5•6•Updated Jul 9, 2024Jul 9, 2024

    • ribiosAnnotation

      Public
      Annotate features (genes, mRNAs, proteins, ...) with ribios
      R
      •1•0•2•0•Updated Jul 7, 2024Jul 7, 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

    • PMDA-Summer-School

      Public
      Public website of Roche PMDA Summer School
      GNU General Public License v3.0
      •3•2•0•0•Updated May 17, 2024May 17, 2024

    • GeMS

      Public
      Gene set management system based on a MongoDB backend
      Python
      •1•3•0•1•Updated Apr 17, 2024Apr 17, 2024

    • MelanomaCITResponse_scRNAseq_TILandPBMC_publication

      Public
      This repository includes notebooks utilized to produce results for the publication "Myeloid-T cell interplay, cell state transitions and checkpoint inhibitor response in melanoma"
      Jupyter Notebook
      •0•1•0•0•Updated Apr 8, 2024Apr 8, 2024

    • CD8-immune-phenotype-paper-supplementary

      Public
      Supplementary source code for the CD8 immune phenotype publication
      Jupyter Notebook
      •0•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • GLOC-hep_distr_and_system_param

      Public
      R
      •0•0•0•0•Updated Dec 26, 2023Dec 26, 2023

    • ribiosNGS

      Public
      Next-generation sequencing data analysis with ribios
      R
      •2•2•5•0•Updated Oct 3, 2023Oct 3, 2023

    • refsnake

      Public
      Snakemake workflow to generate reference genomes and annotations
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 20, 2023Sep 20, 2023

    • dynamic-form

      Public
      Python
      •
      GNU General Public License v3.0
      •0•2•0•2•Updated Sep 12, 2023Sep 12, 2023

    • cd8ippred

      Public
      R package to predict immune phenotypes from RNA-Seq
      R
      •
      Other
      •0•0•0•0•Updated Sep 5, 2023Sep 5, 2023

    • ribiosPlot

      Public
      Data transformation and visualization with the ribios suite
      R
      •1•1•0•0•Updated Sep 1, 2023Sep 1, 2023

    • ribiosExpression

      Public
      Data structure and functions for gene expression analysis
      R
      •1•0•1•0•Updated Aug 29, 2023Aug 29, 2023

    • ngs-tools

      Public
      Helper tools written in C, Bash, Python, and R for next-generation sequencing data analysis.
      C
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 14, 2023Aug 14, 2023

    • sapiens

      Public
      Gene Signature Annotation Pipeline
      Python
      •0•0•0•0•Updated May 17, 2023May 17, 2023

    • metadata-registration-api

      Public
      A flask microservice to register and manage metadata via an API.
      Python
      •
      GNU General Public License v3.0
      •1•1•0•3•Updated May 1, 2023May 1, 2023

    • bios-to-go

      Public
      Static files of the BIOS, aka Bioinfo-C, library
      C
      •
      GNU Lesser General Public License v3.0
      •0•2•0•0•Updated Apr 25, 2023Apr 25, 2023

    • BP40087_paper_supplementary_code

      Public
      Supplementary source code related to the clinical trial BP40087
      R
      •1•0•0•0•Updated Apr 17, 2023Apr 17, 2023

    • microbiome10XVisium

      Public
      R
      •
      Other
      •0•2•0•0•Updated Apr 13, 2023Apr 13, 2023