Data and code for Guo et al., Single-cell virology

This repository includes the datsets and analysis pipeline of Guo et al., "Single-cell virology: on-chip investigation of viral infection dynamics".

The file SCV_data_information_short.xlsx includes detailed information about the samples including the conditions of the experiment and the threshold intensity value used in the experiments.

The file data_figure_relations.txt includes information that links datasets with figures.

Folders

• codeSicegar: analysis pipeline files, built on top of the R package sicegar
• rawData: raw intensity measurements from single-cell infections
• tidyData: same raw intensity files in tidy form
• detailedSicegarResults: all the outputs of the sicegar package for each sample set
• finalResultsRMarkDown: various files: html files that show comparisons of multiple datasets, files that includes all the outputs of sicegar package combined with experimental condition details, and summary tables that summarize sicegar outputs
• supplemental_text: supplemental text for this manuscript