Engineering RNA export for measurement and manipulation of living cells

Description

Overview This repository contains code and data for analysis and plotting related to the development of synthetic RNA export systems and their application for non-destructive measurement of cell dynamics and delivering RNA from cell to cell. Citation If you use this code, please cite this paper. Horns et al., Engineering RNA export for measurement and manipulation of living cells, Cell 186 (2023). Organization The repository is organized into directories that contain code and data, as described below. analysis: Analysis code to generate figures. imaging_data: Images used for analysis. pipelines: Pipelines for preprocessing sequencing reads. preprocessed_data: Preprocessed data (qPCR, flow cytometry, sequencing, etc.). raw_sequencing_data: Sequencing reads. resources: Software and reference data. sequencing_data_preprocessing: Working directory for pipelines for preprocessing sequencing reads. Environment The primary environment uses Python 3.7.7 and is specified in analysis/environment.yml. Use of the Conda package manger is recommended. Disclaimer This project is not maintained. Software is provided as is and requests for support may not be addressed. Contact If you have questions or comments, please contact Felix Horns at rfhorns@gmail.com.

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External Files

Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/8zr8w-t0f77/

Additional details