https://github.com/epigen/scifirna-seq_publication
The million-scale method for single-cell analysis
https://github.com/epigen/scifirna-seq_publication
Last synced: 10 months ago
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The million-scale method for single-cell analysis
- Host: GitHub
- URL: https://github.com/epigen/scifirna-seq_publication
- Owner: epigen
- Created: 2018-07-27T15:58:08.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2023-07-06T22:20:07.000Z (almost 3 years ago)
- Last Synced: 2024-10-30T23:52:13.531Z (over 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 26.3 MB
- Stars: 10
- Watchers: 18
- Forks: 0
- Open Issues: 6
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Metadata Files:
- Readme: README.md
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README
scifi-RNA-seq publication
===================
The repository with source code used in the development of [scifi-RNA-seq (Datlinger et al.)](https://www.biorxiv.org/content/10.1101/2019.12.17.879304v1).
> :warning: 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](https://github.com/epigen/scifiRNA-seq).
This repository contains [scripts used in the processing of data and its analysis](src/). For processing the data, the [Makefile](Makefile) runs discrete steps, but a full run can be done using the [submission script](scifi).
Metadata registering the experiments and their barcode annotation is [also avaialable](metadata/), and software required is listed in the [requirements file](requirements.txt).
Scripts used in the downstream analysis of the data are:
- [monte_carlo_simulations.py](src/monte_carlo_simulations.py): for the theoretical "best-case scenario" simulation experiments;
- [droplet_modeling.py](src/droplet_modeling.py): for the modeling of the Chromium device and prediction of collision rates;
- [analysis.4lines_CROP-seq.py](src/analysis.4lines_CROP-seq.py): for the cell line mixture and CROP-seq experiments;
- [analysis.PBMC_Tcell.py](src/analysis.PBMC_Tcell.py): for the experiments with primary human data;
- [method_comparison.ipynb](src/method_comparison.ipynb): for the comparison across various methods (10X Chromium, sci-rna, sciPlex, SPLiT-seq, and scifi-RNA-seq).