serratus-reactivation-screen

Last updated: June 3, 2023

Step 1 - pull libraries mapping to viruses using ViralZone and Serratus

The serratus_data_setup folder contains the workflow, including all relevant substeps to systematically query Serratus through the API based on viruses annotated through ViralZone.

Step 2 - annotate libraries with relevant meta data.

The analysis_code folder contains necessary R scripts for post-processing the outputs of the serratus_data_setup to reproduce relevant supplementary tables and figures associated with our computational screen. These are annotated with the GEOquery::getGEO function.

Other notes

The metadata folder contains thousands of .soft files used to pull the submitter-associated metadata. These were downloaded programmatically using the GEOquery::getGEO() function in the analysis_code/02_hhv6_followup.R folder.

The output folder represents finalized, processed data, including plots used in the Lareau et al. HHV-6 manuscript.

Mapping to supplemental tables

Here, we explicitly map the files in output used to create the extended data tables found in the manuscript.

Extended Data Table 1 = output/Serratus_hits_all_viruses.tsv
Extended Data Table 2 = output/Serratus_libraries_all_hits_reactivation.tsv
Extended Data Table 4 = output/tcell_hits_per_virus.tsv
Extended Data Table 7 = output/iPSC_hits_per_virus.tsv

Other useful tables

All iPSC SRAs = output/all_iPSC_SRAs.tsv
All Tcell SRAs = output/all_tcell_SRAs.tsv

Note Serratus_libraries_all_hits_reactivation.tsv is for all viruses that can reactivate, the output of the serratus_data_setup folder. all_libraries_reactivation_annotated.tsv includes the annotations of biosamples that we need for plotting / downstream annotation filtering.