Repositories list

• pyviscel

  Public
  Python implementation of VisCello for single-cell RNA-seq visualization

  Python

  •0•0•0•0•Updated Mar 29, 2026Mar 29, 2026

• deMULTIplex2

  Public
  deMULTIplex2: robust sample demultiplexing for scRNA-seq

  scrna-seqstatistical-modelsbioinformatics-algorithms+ 3

  scrna-seqstatistical-modelsbioinformatics-algorithmsdemultiplexingcell-hashingmulti-seq

  R

  •

  Creative Commons Attribution 4.0 International

  •3•19•0•0•Updated Mar 12, 2026Mar 12, 2026

• Concord

  Public
  Python

  •

  MIT License

  •4•43•2•0•Updated Jan 26, 2026Jan 26, 2026

• Concord_benchmark

  Public
  Benchmarking script for CONCORD.

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •0•3•0•0•Updated Oct 29, 2025Oct 29, 2025

• Concord_documentation

  Public
  Full documentation for Concord.

  HTML

  •1•0•0•0•Updated Sep 9, 2025Sep 9, 2025

• jdm-DECIPHER-2024

  Public
  Analysis code used for Rabadam et al. JCI Insight, 2024.

  R

  •1•0•0•0•Updated May 21, 2025May 21, 2025

• MULTI-ATAC

  Public
  Companion code for Conrad, et al.

  R

  •

  MIT License

  •1•1•0•0•Updated Mar 6, 2025Mar 6, 2025

• GutSPV

  Public
  SPV model of intestinal villus clustering

  Python

  •1•0•0•0•Updated Jan 16, 2025Jan 16, 2025

• deMULTIplex2-benchmark

  Public
  Code for benchmarking the performance of demultiplex2.

  R

  •0•0•0•0•Updated Oct 11, 2023Oct 11, 2023

• BCC_Lattice_Model

  Public
  MATLAB

  •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

• Organoid_Image_Processing

  Public
  MATLAB scripts for the processing and quantification of mammary organoid images

  MATLAB

  •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

• deMULTIplex2_test_data

  Public
  test datasets for deMULTIplex2

  1•1•0•0•Updated Jun 10, 2023Jun 10, 2023

• DoubletFinder

  Public
  R package for detecting doublets in single-cell RNA sequencing data

  R

  •124•0•0•0•Updated May 10, 2022May 10, 2022

• MULTI-seq

  Public
  R implementation of MULTI-seq sample classification workflow

  R

  •11•1•0•0•Updated Dec 6, 2021Dec 6, 2021