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    90 repositories

    • scran

      Public
      Clone of the Bioconductor repository for the scran package.
      single-cell-rna-seqbioconductor-packagehuman-cell-atlas
      single-cell-rna-seqbioconductor-packagehuman-cell-atlas
      R
      •23•46•19•1•Updated Feb 25, 2026Feb 25, 2026

    • miloDE

      Public
      Framework for sensitive DE testing (using neighbourhoods)
      R
      •
      Other
      •5•77•6•0•Updated Nov 11, 2025Nov 11, 2025

    • miloR

      Public
      R package implementation of Milo for testing for differential abundance in KNN graphs
      R
      •
      GNU General Public License v3.0
      •25•421•18•1•Updated Sep 4, 2025Sep 4, 2025

    • DropletUtils

      Public
      Clone of the Bioconductor repository for the DropletUtils package.
      single-cell-rna-seqbioconductor-packagehuman-cell-atlas
      single-cell-rna-seqbioconductor-packagehuman-cell-atlas
      R
      •28•64•14•1•Updated Aug 27, 2025Aug 27, 2025

    • COSICC

      Public
      COSICC R package
      R
      •
      Other
      •0•1•0•0•Updated Jun 23, 2025Jun 23, 2025

    • analysis_chimera_data

      Public
      Systematic characterisation of perturbations in complex developing cell populations reveals mechanisms underpinning development and disease
      HTML
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • ExtendedMouseAtlas

      Public
      0•1•0•0•Updated Feb 24, 2025Feb 24, 2025

    • oor_benchmark

      Public
      A sandbox for benchmarking detection of out-of-reference cells in single-cell genomics data
      Python
      •
      MIT License
      •2•14•1•0•Updated Oct 21, 2024Oct 21, 2024

    • cydar

      Public
      Clone of the Bioconductor repository for the cydar package.
      R
      •2•1•0•0•Updated Sep 6, 2024Sep 6, 2024

    • BE_perturb_seq_drug_resistance

      Public
      HTML
      •1•0•0•0•Updated Aug 26, 2024Aug 26, 2024

    • CELLOseq

      Public
      Transposable element expression at unique loci in single cells with CELLO-seq
      Shell
      •
      MIT License
      •4•11•1•0•Updated Jun 17, 2024Jun 17, 2024

    • EmptyDropsMultiome

      Public
      Removing empty droplets in multiome datasets
      R
      •
      Other
      •0•17•0•0•Updated Jun 3, 2024Jun 3, 2024

    • EmptyDropsMultiome2023_final

      Public
      R
      •0•3•1•0•Updated Apr 23, 2024Apr 23, 2024

    • miloDE_tutorials

      Public
      this folder stores Rmds and htmls to miloDE vigenettes
      HTML
      •0•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • miloDE_analysis

      Public
      Folder contains scripts to generate and analyse data for miloDE
      HTML
      •0•2•0•0•Updated Mar 19, 2024Mar 19, 2024

    • hbca

      Public
      Code used to process the data of the HBCA project
      R
      •6•33•1•0•Updated Feb 9, 2024Feb 9, 2024

    • MouseGastrulationData

      Public
      Clone of the Bioconductor repository for the MouseGastrulationData package.
      R
      •2•13•0•0•Updated Jan 24, 2024Jan 24, 2024

    • sagenet

      Public
      Spatial reconstruction of dissociated single-cell data
      Jupyter Notebook
      •
      MIT License
      •2•19•3•0•Updated Jan 12, 2024Jan 12, 2024

    • sagenet_paper

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 11, 2023Dec 11, 2023

    • scSNV-seq

      Public
      HTML
      •
      GNU General Public License v3.0
      •2•3•0•0•Updated Oct 16, 2023Oct 16, 2023

    • oor_design_reproducibility

      Public
      Jupyter Notebook
      •1•16•1•0•Updated Sep 1, 2023Sep 1, 2023

    • CTLstimulation

      Public
      Analysis of RNAseq and mass spectrometry data of stimulated cytotoxic T lymphocytes to understand the role of transcription
      MIT License
      •0•0•0•0•Updated Aug 21, 2023Aug 21, 2023

    • geneBasisR

      Public
      R package for gene selection using k-NN graphs.
      R
      •
      MIT License
      •4•13•5•0•Updated Jun 12, 2023Jun 12, 2023

    • leftRight_asymmetry

      Public
      HTML
      •0•0•0•0•Updated Apr 26, 2023Apr 26, 2023

    • RabbitGastrulation2022

      Public
      Jupyter Notebook
      •4•5•0•0•Updated Apr 4, 2023Apr 4, 2023

    • StabMap2021

      Public
      Analysis scripts for 'StabMap: Mosaic single cell data integration using non-overlapping features'
      R
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Feb 28, 2023Feb 28, 2023

    • MouseThymusAgeing

      Public
      MouseThymusAgeing data package
      R
      •0•0•0•0•Updated Feb 14, 2023Feb 14, 2023

    • SpatialMouseAtlas2020

      Public
      Data processing and analysis scripts for our spatial profiling of embryos using seqFISH
      R
      •
      MIT License
      •5•16•1•0•Updated Feb 10, 2023Feb 10, 2023

    • StabMap

      Public
      Mosaic single cell data integration using non-overlapping features
      R
      •0•38•4•0•Updated Sep 20, 2022Sep 20, 2022

    • Tumorigenesis2018

      Public
      R
      •2•4•0•0•Updated Sep 8, 2022Sep 8, 2022