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.
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).