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1. scRNAseq_Normalization scRNAseq_Normalization Public

   Pipeline to normalize and benchmark single-cell RNA-sequencing (scRNAseq) data.

   Python

2. SCDemultiplexingPipeline SCDemultiplexingPipeline Public

   A fast pipeline for demultiplexing highly multiplexed single-cell data (like Combinatorial Indexing) and creating a SC-FEATURE matrix. The tool is readily applicable to any combination of barcodes.…

   C++

3. scMRA_Tutorial scMRA_Tutorial Public

   HTML

4. scmra_analysis scmra_analysis Public

   This repository contains all the code for the scMRA/scCNR paper 'Reconstructing and comparing signal transduction networks from single cell protein quantification data'.

   Jupyter Notebook

5. SCDemultiplexingGUI SCDemultiplexingGUI Public

   GUI for fast and effecient demultipelxing of any single-cell data. RNAseq mapping ahs to be done independantly.

   C++

6. SCProteinNormalization SCProteinNormalization Public

   Method to normalize single-cell protein count data. We find and optimal balance between normalizing away library size while at the same time keeping the cov(protein, normFactor) as low as possible.

   Jupyter Notebook