This repository contains SCITO-seq package for demultiplexing and resolving single cell data from SCITO-seq experiments. It also contains manuscript-related CyTOF data, SCITO-seq data and code and notebooks used for analysis.
To get the data you need to install Git LFS and git clone this repository. Downloading ZIP will only download pointers to the data.
We are currently working on integrating python SCITO-seq package into the unified workflow.
paper/code - R code and jupyter notebooks demonstrating SCITO-seq data analysis
paper/CyTOF - CyTOF data
paper/SCITOseq_counts - count matrices (outputs of cellranger count)
Tutorial.md - detailed SCITO-seq data analysis workflow as presented in the manuscript
Package nero featured in some Jupyter notebooks is an unreleased package for handling single cell data. For your analysis you can exclude it and filter demuxlet outputs with pandas.DataFrame methods.