scifi-RNA-seq publication

The repository with source code used in the development of scifi-RNA-seq (Datlinger et al.).

⚠️ This repository includes source code to reproduce the analysis in the manuscript and won't be maintained to support the analysis of other datasets. For that, see the general-purpose data processing pipeline of scifi-RNA-seq data.

This repository contains scripts used in the processing of data and its analysis. For processing the data, the Makefile runs discrete steps, but a full run can be done using the submission script.

Metadata registering the experiments and their barcode annotation is also avaialable, and software required is listed in the requirements file.

Scripts used in the downstream analysis of the data are:

• monte_carlo_simulations.py: for the theoretical "best-case scenario" simulation experiments;
• droplet_modeling.py: for the modeling of the Chromium device and prediction of collision rates;
• analysis.4lines_CROP-seq.py: for the cell line mixture and CROP-seq experiments;
• analysis.PBMC_Tcell.py: for the experiments with primary human data;
• method_comparison.ipynb: for the comparison across various methods (10X Chromium, sci-rna, sciPlex, SPLiT-seq, and scifi-RNA-seq).