Repository with the analysis of two kidney fibrosis models in mouse
This repository contains scripts to analyze the data, produce the final figures, and helpers for submission.
Scritpts:
create_data_citation.R: Write final files for data citation reference in the paper.create_geo_files.R: Write final files to upload to GEO database.create_multiassay_obj.R: create MultiExperiment R object to access all the data from a single point. Used as well in the Rshiny app.figures.R: create final figures for the paper.metrics.R: summarize sequencing metrics for the paper.prepare2app.R: create all the objects needed for the Rshiny app.
Folders:
bcbio: contains the config file used with bcbio-nectgen to analyze the data.browser_app: contains the Rshiny app itself.data_citation: contains the final table cited in the paper.figures: contains all the figures used in the paper.reports: contains the individual reports for each type of data and mouse model.tables: contains the data generated by the reports.
Contributors:
- Lorena Pantano, Ph.D
- Mira Pavkovic, Ph.D