README.md

In rosscm/multiGIviewer: Multi-screen genetic interaction viewer

# multiGIviewer An interactive R {shiny} web application built with the {golem} framework to view multi-screen genetic interaction data

# Contents - [Usage](#usage) - [Inputs](#inputs) - [Outputs](#outputs) # Usage Watch this short demo on how to use `multiGIviewer` to view replicated genetic interactions (qGI scores) across two or more CRISPR screens of interest.  # Inputs | 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 \[*optional*\] | # Outputs #### Plot | 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 | #### Table | 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 |

rosscm/multiGIviewer documentation built on Dec. 22, 2021, 6:17 p.m.