hit selection module #191
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hit selection module #191
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LaurenceKuhl
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LaurenceKuhl
commented
Sep 2, 2024
LaurenceKuhl
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Sep 2, 2024
WackerO
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Sep 4, 2024
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| min <- 0 | ||
| max <- ${hit_selection_iteration_nb} | ||
| steps <- max - min |
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If min is always 0, this is not really necessary
| steps <- max - min | ||
| hit.genes.last <- NULL | ||
| final_results <- list() # Initialize as an empty list | ||
| for(i in 1:steps) { |
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This can accordingly be changed as well
Co-authored-by: WackerO <[email protected]>
Co-authored-by: WackerO <[email protected]>
mirpedrol
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Sep 12, 2024
| - ([MAGeCK test](https://sourceforge.net/p/mageck/wiki/usage/#test)) | ||
| - ([MAGeCK mle](https://sourceforge.net/p/mageck/wiki/Home/#mle)) | ||
| - ([BAGEL2](https://github.com/hart-lab/bagel)) | ||
| - ([DrugZ](https://github.com/hart-lab/drugz)) |
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Should this go under point 5?
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Actually no it's also a gene essentiality analysis but only on drug treated cell lines. It does something similar to MAGeCK MLE
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| ## :warning: The hitselection algorithm is for the moment developed only for KO screens and requires the library to map to genes with an Homosapiens EntrezID. | ||
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| ## :warning: Please be advised that the Hitselection algorithm is time intensive and will make the pipeline run longer |
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To show a formatted warning box on the webside the notation is the following:
> [!WARNING]
> The hitselection algorithm is for the moment developed only for KO screens and requires the library to map to genes with an Homosapiens EntrezID.
> [!WARNING]
Please be advised that the Hitselection algorithm is time intensive and will make the pipeline run longer
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This PR aims to add a new feature : hit selection. The aim would be to run an algorithm on found gene essentials and determine a p-value cutoff based on the degree of protein protein interaction network.
nf-core/crisprseq runs MAGeCK RRA, MAGeCK MLE, BAGEL2 or DRUGZ so I've plugged HITSELECTION after each of these processes and added a parameter giving the user the option to run hitselection or not.
It bases itself on an R script in the module hitselection.nf and on 2 assets : hgnc_complete_set and biogrid_hgncid