Data repository for "Orobas: A Computational Approach for Scoring and Analysis of Quantitative Chemical-Genetic Interactions from CRISPR-Cas9 Screens"
Authors/Creators
-
1.
University of Minnesota
Description
This repository contains an example input data and the corresponding outputs generated after applying the Orobas protocol. Orobas is an R tool (with Python modules) for scoring and analyzing chemical-genetic CRISPR screening data.
The data folder includes the raw reads data from chemical–genetic screens (Dataset_all_readcounts.txt), which serve as the primary data source. These screens were produced and published by Olivieri et al. (2020) [1]. The original datasets were downloaded from here under the ‘CRISPR screen readcount files’ link and merged into a single matrix. This folder also contains two metadata tables—screen_replicate_map_table.tsv and condition_control_map_table.tsv—constructed based on the input data and required to run the protocol.
The output folder contains all results produced by the Orobas when applied to the Olivieri et al. dataset.
The Orobas can be downloded from https://github.com/csbio/orobas. Two example scripts to reproduce the outputs can be found here.
[1] Olivieri, M., Cho, T., Álvarez-Quilón, A., Li, K., Schellenberg, M.J., Zimmermann, M., Hustedt, N., Rossi, S.E., Adam, S., Melo, H., et al. (2020). A Genetic Map of the Response to DNA Damage in Human Cells. Cell 182, 481-496.e21. https://doi.org/10.1016/j.cell.2020.05.040.
Files
Dataset_all_readcounts.txt
Files
(545.2 MB)
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Additional details
Software
- Repository URL
- https://github.com/csbio/orobas
- Programming language
- R , Python