rothSGA: SGA analysis tools for the Rothstein Lab.

In matthieu-haudiquet/rothSGA: Rothstein Lab SGA Analysis Tools

Description

Tools in this package are provided to standardize common steps in the quantification of genetic interactions derived from Synthetic Genetic Array (SGA) colony growth experiments.

Details

Groups of SGA experiments performed in parallel at the same time are considered part of the same "Batch". We recommend processing each batch independently using approximately the following workflow:

1. Record colony growth (ideal incubation time will depend on several factors including: strain background, media, temperature, pinning procedure). We recommend using a flatbed scanner with a transparency lid (e.g. the Micotek 9800XL can scan 9 standard rectangular plates.)

2. Annotate plates in images with screenmill::annotate which integrates with the Rothstein Lab's annotation database rothfreezer::rothfreezer

3. Locate colony grid and determine plate cropping coordinates with screenmill::calibrate

4. Review plates to exclude regions with contamination or failed pinnings with screenmill::review

5. Measure colonies with screenmill::measure

6. Normalize spatial and plate effects with rothSGA::normalize_spatial_effect and rothSGA::normalize_plate_effect

7. Run quality control checks with e.g. rothSGA::check_dead_strains and rothSGA::check_self_crosses

This pipeline can be quickly generated using rothSGA::new_batch_report which generates an Rmarkdown report from a standard template.

matthieu-haudiquet/rothSGA documentation built on May 14, 2019, 11:28 a.m.