Command Arguments
Subcommands
crispr_screen has two subcommands:
testagg
test is used to perform the sgRNA-level differential abundance tests and then aggregate the results to the gene-level.
test by default will perform a gene-level aggregation as well, but can be skipped with the --skip-agg flag.
agg is used to just perform the gene-level aggregation on a precalculated differential abundance matrix.
Take a look at the results.sgrna.tsv file to see the expected file format required. Column names can
be provided as well - details can be found by running crispr_screen agg --help
Arguments
Required
The three required arguments are as follows:
| Argument | Description |
|---|---|
| input | Filepath of the input count matrix |
| controls | Labels for the control samples (can take multiple space-separated values) |
| treatments | Labels for the treatment samples (can take multiple space-separated values) |
Optional Arguments
These arguments are optional and may change the configuration of the analysis.
For further details on them please run:
crispr_screen test --help
| Argument | Description |
|---|---|
| output | Prefix of the output sgRNA and gene result dataframes |
| norm | Normalization method to use |
| agg | Gene aggregation method to use |
| correction | Multiple hypothesis correction to use |
| model-choice | Which least squares model to fit |
| alpha | The alpha threshold parameter for aRRA algorithm |
| permutations | The number of permutations to perform in aRRA algorithm |
| no-adjust-alpha | Use flag to have fixed alpha, otherwise an empirical one will be calculated from provided alpha. |
| ntc-token | The token string to search for non-targeting controls (if INC) |