Repositories list

• sopa

  Public
  Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •19•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• amex_merfish_spaceolotl

  Public
  Python

  •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

• analysis_template

  Public template
  Simple template repo for single-cell/spatial analysis

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 10, 2024Nov 10, 2024

• RNAseq_tutorial

  Public
  7•17•0•0•Updated Oct 16, 2024Oct 16, 2024

• morphodynamics_human_brain_organoid

  Public
  Jupyter Notebook

  •1•1•0•0•Updated Sep 13, 2024Sep 13, 2024

• moscot

  Public
  Multi-omic single-cell optimal transport tools

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •9•0•0•0•Updated Jul 26, 2024Jul 26, 2024

• Tangram

  Public
  Spatial alignment of single cell transcriptomic data.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •51•0•0•0•Updated Jul 3, 2024Jul 3, 2024

• scMultiome_analysis_vignette

  Public
  Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis

  tutorialsingle-cell-rna-seqsingle-cell-analysis+ 3single-cell-atac-seqsingle-cell-multiomicsbioinformatics

  13•48•5•0•Updated Apr 22, 2024Apr 22, 2024

• Pando

  Public
  Multiome GRN inference.

  transcriptomicssingle-cellepigenomics

  R

  •

  MIT License

  •21•113•19•2•Updated Apr 19, 2024Apr 19, 2024

• scRNAseq_analysis_vignette

  Public
  Tutorial for scRNA-seq data analysis beginners using R

  bioinformaticstutorialsingle-cell-rna-seq+ 1single-cell-analysis

  58•162•2•0•Updated Apr 18, 2024Apr 18, 2024

• organoid_epigenomics

  Public
  R

  •1•7•1•0•Updated Apr 12, 2024Apr 12, 2024

• simspec

  Public
  Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)

  batch-correctionsingle-cell-analysis

  R

  •3•30•5•0•Updated Mar 6, 2024Mar 6, 2024

• VoxHunt

  Public
  VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

  single-cellorganoids

  HTML

  •

  MIT License

  •5•42•2•0•Updated Mar 1, 2024Mar 1, 2024

• latent-lego

  Public
  Latent spaces for single cells

  Jupyter Notebook

  •

  MIT License

  •0•22•0•0•Updated Oct 31, 2023Oct 31, 2023

• iTracer_analysis

  Public
  Scripts to analyze iTracer data

  HTML

  •1•9•0•0•Updated Oct 20, 2023Oct 20, 2023

• itraceR

  Public
  The R package to preprocess barcode and scar data of iTracer

  R

  •0•0•0•0•Updated Oct 16, 2023Oct 16, 2023

• organoid_regulomes

  Public
  Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids

  R

  •8•25•3•0•Updated Aug 8, 2023Aug 8, 2023

• spatial_multimodal_retinal_organoid

  Public
  R

  •1•9•0•0•Updated Apr 7, 2023Apr 7, 2023

• scRNAseq_comparison_vignette

  Public
  Tutorial of condition comparison analysis of scRNA-seq data

  bioinformaticstutorialsingle-cell-rna-seq+ 1single-cell-analysis

  1•8•0•0•Updated Jul 18, 2022Jul 18, 2022

• ASD_CHOOSE

  Public
  Scripts to reproduce the figures from the CHOOSE study

  R

  •1•2•0•0•Updated May 16, 2022May 16, 2022

• primate_cerebral_organoids

  Public
  Reusable scripts and functions archive for the paper "Organoid single-cell genomic atlas uncovers human-specific features of brain development" (https://www.nature.com/articles/s41586-019-1654-9)

  R

  •3•33•3•0•Updated Aug 2, 2021Aug 2, 2021

• voxhunt_reproducibility

  Public
  R markdown scripts to reproduce analyses from the VoxHunt paper

  0•0•0•0•Updated Mar 8, 2021Mar 8, 2021

• jupytext

  Public
  Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts

  Python

  •

  MIT License

  •389•1•0•0•Updated Jan 18, 2021Jan 18, 2021