An interactive R {shiny} web application built with the {golem} framework to view multi-screen genetic interaction data
Watch this short demo on how to use multiGIviewer to view replicated
genetic interactions (qGI scores) across two or more CRISPR screens of
interest.
| Parameters | Values | Properties |
|---|---|---|
| Dataset | GIN_20210406, GIN_20210107, GIN_20201129, CHEM_20210218, CHEM_20210218_GIN_20210406 | qGI scores for 280 (GIN_20210406), 257 (GIN_20210107), 247 (GIN_20201129), 68 (CHEM_20210218), 348 (CHEM_20210218) & (GIN_20210406) screens [required; default GIN_20210406] |
| Screens | screens IDs | list of all screens in selected dataset; two or more screens need to be selected to view replicated interactions [required] |
| Media conditions(s) | min, rich, pyro and/or DMSO | media type used to define wildtype single mutant fitness; more than one can be selected if screens were done in different media types [required] |
| FDR threshold | value from 0 to 1 | threshold to define significant genetic interactions; interactions must pass threshold in at least two screens to be shown [required; default 0.2] |
| Positive colour | HEX colour codes | colour to fill darkest positive points [optional; default #FAE057] |
| Negative colour | HEX colour codes | colour to fill darkest negative points [optional; default #61C2FA] |
| Plot labels | gene symbols | comma separated (character sensitive) list of genes to label on plot [optional; default top ten positive and negative interactions] |
| Label type | Text or Padded box | method to draw plot labels; padded box wraps text in a white box to better visualize labels [optional; default Text] |
| Reference line(s) | y=x, x=0 and/or y=0 | selection of reference lines to draw on plot [optional] |
| Elements | Properties |
|---|---|
| Fitness HAP1 wildtype [LFC] (x-axis) | corresponds to mean_wtLFC column |
| Fitness HAP1 knockout [LFC] (y-axis) | corresponds to mean_koLFC column |
| Genetic interaction in n screens (fill) | corresponds to n_sig column |
| Mean qGI score (size) | corresponds to mean_qGI column |
| Columns | Properties |
|---|---|
| gene | gene interaction |
| mean_qGI | mean qGI score of interaction across selected screens |
| min_FDR | minimum qGI FDR value of interaction across selected screens |
| mean_wtLFC | mean wildtype dropout effect (log2-foldchange) across selected media condition(s) |
| mean_koLFC | mean knockout dropout effect (log2-foldchange) across selected screens |
| n_sig | number of times positive or negative interaction is significant across selected screens |
| screen_sig | list of screens where interaction is significant |