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@cbib Centre de Bioinformatique de Bordeaux

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    26 repositories

    • snakemake_tcga_survival

      Public
      R
      •1•0•0•0•Updated Jul 7, 2026Jul 7, 2026

    • TrialMatchAI

      Public
      TrialMatchAI leverages large language models to streamline clinical trial matching by evaluating patient-specific clinical characteristics against trial eligibi…
      pythonartificial-intelligencecancer-genomics
      pythonartificial-intelligencecancer-genomicsclinical-trialspersonalized-medicinepersonalized-recommendationlarge-language-models
      Python
      •
      Other
      •13•31•0•0•Updated Jul 6, 2026Jul 6, 2026

    • DeconvoliSTa

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Jul 6, 2026Jul 6, 2026

    • COBRA

      Public
      Multi-omics data integrative web application for plant-virus resistance gene
      HTML
      •3•2•0•1•Updated May 28, 2026May 28, 2026

    • Reproduce_cSCC_GeoMx_HTGseq

      Public
      R
      •0•0•0•0•Updated May 6, 2026May 6, 2026

    • uncertainty_aware_lnclassifier

      Public
      A Snakemake pipeline benchmarking transcript classification tools
      Jupyter Notebook
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • rep_extraction_pipeline

      Public
      Snakemake pipeline to extract repetitive elements features using Repeatmasker and custom scripts.
      Python
      •1•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • nbd_extraction_pipeline

      Public
      About Snakemake pipeline to extract Non-B DNA motif features using gfa, G4Discovery and custom scripts.
      Jupyter Notebook
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • LncDC

      Public
      LncDC: a machine-learning based tool for long non-coding RNA detection from RNA-Seq data
      Python
      •
      MIT License
      •4•0•0•1•Updated Mar 29, 2026Mar 29, 2026

    • beta_vae_lnclassifier

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • linda

      Public
      Web application for managing experimental and environmental metadata for plant experiments
      nodejsphenotypingarangodb
      nodejsphenotypingarangodbontologiesangular8miappe
      TypeScript
      •
      MIT License
      •0•2•13•19•Updated Feb 11, 2026Feb 11, 2026

    • mRNN

      Public
      mRNN is an implementation of a Gated Recurrent Unit (GRU) network for classification of transcripts as either coding or noncoding.
      Python
      •11•0•0•0•Updated Jan 18, 2026Jan 18, 2026

    • DIMet

      Public
      Differential analysis of targeted Isotope-labeled Metabolomics data
      pythonmetabolomicsdifferential-expression
      pythonmetabolomicsdifferential-expressionisotope-labeling-experimentsmetabolomics-pipeline
      Python
      •
      MIT License
      •2•5•0•0•Updated Jan 15, 2026Jan 15, 2026

    • Seurat-Integrate

      Public
      R package expanding integrative analysis capabilities of Seurat by providing seamless access to popular integration methods and to an integration benchmarking t…
      scrna-seqdata-integrationbatch-effects
      scrna-seqdata-integrationbatch-effectssingle-cell-genomicssingle-cell-rna-seqseurat
      R
      •
      Other
      •3•34•4•0•Updated Sep 3, 2025Sep 3, 2025

    • virhunter

      Public
      Deep Learning method for novel virus detection in sequencing data
      Python
      •
      Other
      •2•10•1•0•Updated Mar 19, 2025Mar 19, 2025

    • ProteomX

      Public
      Statistical and Functional analysis and interpretation of proteomics data
      Python
      •
      MIT License
      •1•0•30•6•Updated Sep 4, 2024Sep 4, 2024

    • TraceGroomer

      Public
      Format and normalise tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet analysis.
      Python
      •
      MIT License
      •1•2•0•0•Updated Aug 6, 2024Aug 6, 2024

    • TempAI

      Public
      Python
      •0•1•0•0•Updated Jul 18, 2024Jul 18, 2024

    • dypfish

      Public
      Python library for statistical analysis of mRNA and protein distributions in fluorescent microscopy images
      Python
      •
      Other
      •2•3•8•5•Updated Oct 3, 2023Oct 3, 2023

    • SalienceNet

      Public
      Python
      •
      MIT License
      •1•8•0•0•Updated Jul 31, 2023Jul 31, 2023

    • tflex

      Public
      R
      •0•0•0•0•Updated May 10, 2023May 10, 2023

    • decontaminator

      Public
      deep learning contamination filtering tool
      deep-learninggenomicsrnaseq
      deep-learninggenomicsrnaseqviruses
      Python
      •
      Other
      •0•0•0•0•Updated Jan 22, 2023Jan 22, 2023

    • DeepMeta

      Public
      Deep Learning network to segment lungs and metastases in mouse MRI images.
      Python
      •
      MIT License
      •1•1•0•1•Updated Jul 20, 2022Jul 20, 2022

    • DeepSpot

      Public
      DeepSpot is a deep learning method for the enhancement of mRNA fluorescent spots in microscopy images
      Python
      •
      Other
      •3•15•0•0•Updated Dec 1, 2021Dec 1, 2021

    • MICADo

      Public
      Looking for mutations in PacBio cancer data: an alignment-free method
      Python
      •
      Other
      •2•8•1•0•Updated Nov 10, 2016Nov 10, 2016

    • MIX

      Public
      MIX: Combining multiple assemblies from NGS data
      Python
      •6•13•4•0•Updated Apr 14, 2016Apr 14, 2016
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