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    30 repositories

    • SingleMoleculeGenomicsIO

      Public
      Reading of single molecule genomics data formats into SummarizedExperiment objects
      R
      •
      Other
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • mutscan

      Public
      Software to process, statistically analyse and visualise deep mutational scanning data
      R
      •
      Other
      •0•14•5•1•Updated Apr 14, 2026Apr 14, 2026

    • intermediate_ggplot2

      Public
      Tips and tricks for intermediate ggplot2 usage
      HTML
      •0•0•1•0•Updated Apr 13, 2026Apr 13, 2026

    • fmicompbio.github.io

      Public
      FMI CompBio's public GitHub repositories
      R
      •1•2•0•0•Updated Apr 13, 2026Apr 13, 2026

    • sketchR

      Public
      An R interface to the subsampling algorithms implemented in python
      R
      •
      Other
      •0•3•0•0•Updated Apr 2, 2026Apr 2, 2026

    • IVMC-protocol

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • einprot

      Public
      Proteomics analysis workflows
      R
      •
      Other
      •1•10•3•0•Updated Mar 22, 2026Mar 22, 2026

    • QuasR

      Public
      This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creat…
      R
      •3•7•4•0•Updated Mar 17, 2026Mar 17, 2026

    • footprintR_book

      Public
      A guide to analyzing single molecule footprinting data with R and footprintR
      TeX
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • ScientificInquiry_ExpDesign

      Public
      HTML
      •0•1•0•0•Updated Feb 1, 2026Feb 1, 2026

    • monaLisa

      Public
      binned motif enrichment analysis and visualisation
      R
      •
      GNU General Public License v3.0
      •7•45•7•0•Updated Jan 27, 2026Jan 27, 2026

    • apical-out-placental-organoids

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jan 12, 2026Jan 12, 2026

    • footprintR

      Public
      Tools for working with single-molecule footprinting data
      genomicsfootprintingepigenomics
      genomicsfootprintingepigenomicssingle-molecule-sequencing
      R
      •
      Other
      •0•2•1•0•Updated Jan 9, 2026Jan 9, 2026

    • ezzarr

      Public
      Thin wrapper around the ez_zarr python package.
      R
      •
      Other
      •0•0•0•0•Updated Nov 13, 2025Nov 13, 2025

    • eisaR

      Public
      Exon-Intron Split Analysis (EISA) in R
      R
      •4•17•0•0•Updated Nov 3, 2025Nov 3, 2025

    • Rbowtie

      Public
      This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. Th…
      C++
      •
      Other
      •0•1•0•0•Updated Oct 30, 2025Oct 30, 2025

    • TabulaMurisSenisData

      Public
      data from the TabulaMuris Senis project
      R
      •
      Other
      •3•3•0•0•Updated Oct 29, 2025Oct 29, 2025

    • Rhisat2

      Public
      R wrapper around the hisat2 aligner.
      C++
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Oct 29, 2025Oct 29, 2025

    • orthos

      Public
      Variance decomposition using conditional variational auto-encoders
      R
      •
      Other
      •0•3•3•0•Updated Oct 2, 2025Oct 2, 2025

    • ez_zarr

      Public
      GIve easy, high-level access to ome-zarr fileset
      ome-zarr
      ome-zarr
      Python
      •
      MIT License
      •2•22•3•0•Updated Sep 22, 2025Sep 22, 2025

    • swissknife

      Public
      Handy code shared in the FMI CompBio group
      R
      •
      GNU General Public License v3.0
      •1•8•1•0•Updated Sep 17, 2025Sep 17, 2025

    • Spombe_TFome

      Public
      Link to rendered reports:
      HTML
      •
      MIT License
      •0•1•0•0•Updated Jul 10, 2025Jul 10, 2025

    • orthosData

      Public
      Data package for `orthos` (https://github.com/fmicompbio/orthos)
      R
      •
      Other
      •0•0•0•0•Updated Jul 5, 2023Jul 5, 2023

    • mutscan_manuscript_2022

      Public
      Code used in the mutscan manuscript (analysis of datasets using mutscan, Enrich2 and DimSum, comparison and visualization)
      R
      •
      MIT License
      •0•1•0•0•Updated Oct 21, 2022Oct 21, 2022

    • adv_singlecell_2022

      Public
      Material for the "Advanced topics in single-cell analysis" course (2022 edition)
      HTML
      •
      GNU General Public License v3.0
      •5•17•0•0•Updated May 20, 2022May 20, 2022

    • fmicompbio.r-universe.dev

      Public
      configure packages for https://r-universe.dev/
      0•0•1•0•Updated Nov 25, 2021Nov 25, 2021

    • griph

      Public
      Graph Inference of Population Heterogeneity.
      R
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Nov 25, 2021Nov 25, 2021

    • PCA_intro2020

      Public
      CSS
      •0•1•0•0•Updated Oct 26, 2020Oct 26, 2020

    • adv_scrnaseq_2020

      Public
      Material for lectures and exercises of the SIB course "Advanced topics in single-cell transcriptomics" (May 2020)
      Jupyter Notebook
      •9•17•0•0•Updated May 29, 2020May 29, 2020

    • SIB_scRNA-seq_Tutorial_2018

      Public
      SIB course teaching concepts for single-cell RNA-seq analysis
      HTML
      •3•7•0•0•Updated Nov 29, 2018Nov 29, 2018
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