Repositories list

• oor_benchmark

  Public
  A sandbox for benchmarking detection of out-of-reference cells in single-cell genomics data

  Python

  •

  MIT License

  •2•12•1•0•Updated Oct 21, 2024Oct 21, 2024

• miloR

  Public
  R package implementation of Milo for testing for differential abundance in KNN graphs

  R

  •

  GNU General Public License v3.0

  •22•342•19•0•Updated Oct 16, 2024Oct 16, 2024

• 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 Oct 16, 2024Oct 16, 2024

• COSICC

  Public
  COSICC R package

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

• DropletUtils

  Public
  Clone of the Bioconductor repository for the DropletUtils package.

  single-cell-rna-seqbioconductor-packagehuman-cell-atlas

  R

  •27•54•14•0•Updated Oct 6, 2024Oct 6, 2024

• cydar

  Public
  Clone of the Bioconductor repository for the cydar package.

  R

  •2•1•0•0•Updated Sep 6, 2024Sep 6, 2024

• scran

  Public
  Clone of the Bioconductor repository for the scran package.

  single-cell-rna-seqbioconductor-packagehuman-cell-atlas

  R

  •22•40•18•1•Updated Sep 5, 2024Sep 5, 2024

• BE_perturb_seq_drug_resistance

  Public
  HTML

  •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

• miloDE

  Public
  Framework for sensitive DE testing (using neighbourhoods)

  R

  •

  Other

  •2•57•4•0•Updated Jul 20, 2024Jul 20, 2024

• CELLOseq

  Public
  Transposable element expression at unique loci in single cells with CELLO-seq

  Shell

  •

  MIT License

  •4•7•1•0•Updated Jun 17, 2024Jun 17, 2024

• EmptyDropsMultiome

  Public
  Removing empty droplets in multiome datasets

  R

  •

  Other

  •0•10•0•0•Updated Jun 3, 2024Jun 3, 2024

• EmptyDropsMultiome2023_final

  Public
  R

  •0•3•0•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

  •5•21•0•0•Updated Feb 9, 2024Feb 9, 2024

• MouseGastrulationData

  Public
  Clone of the Bioconductor repository for the MouseGastrulationData package.

  R

  •2•11•0•0•Updated Jan 24, 2024Jan 24, 2024

• sagenet

  Public
  Spatial reconstruction of dissociated single-cell data

  Jupyter Notebook

  •

  MIT License

  •2•17•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

  •1•3•0•0•Updated Oct 16, 2023Oct 16, 2023

• oor_design_reproducibility

  Public
  Jupyter Notebook

  •1•14•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

  •3•13•4•0•Updated Jun 12, 2023Jun 12, 2023

• leftRight_asymmetry

  Public
  HTML

  •0•0•0•0•Updated Apr 26, 2023Apr 26, 2023

• ExtendedMouseAtlas

  Public
  0•1•0•0•Updated Apr 6, 2023Apr 6, 2023

• RabbitGastrulation2022

  Public
  Jupyter Notebook

  •3•4•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•34•4•0•Updated Sep 20, 2022Sep 20, 2022

• Tumorigenesis2018

  Public
  R

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