sci-Plex-GxE is a platform for combined single-cell genetic and chemical screening at scale. This github repository documens processing pipelines and analysis scripts, including files used for data generation, analysis and interpretation.
The data presented in our manuscript are derived from one of 4 single-cell screens. All raw and processed files can be found on the National Center for Biotechnology Information Gene Expression Ominibus (NCBI GEO) repository under series GSE225775.
| Name | Experiment | GEO Accession | Analysis Scripts |
|---|---|---|---|
| sciPlexGxE_1 | HPRT1 & MMR GxE Screens | GSM7056148 | HPRT1_MMR_GxE_screen |
| sciPlexGxE_2 | Kinome GxE Screen | GSM7056149 | Kinome_GxE_screen |
| sciPlex_3 | GSC Chemical Genomic Screen | GSM7056150 | GSC_chemical_screen |
| sciPlex_4 | Combinatorial Chemical Genomic Screen | GSM7056151 | combinatorial_chemical_screen |
The scripts and code to process the data can be found in the process_from_raw folder. The scripts and code to analyze the data can be found in the folders for each experiment. To access all files and functions used in this study, also download the sci-Plex github repository from Srivatsan, McFaline-Figueroa and Ramani et al. Science 2020.