# Calculate Genetic Interactions for Paired CRISPR Targets

## Documentation for package ‘gimap’ version 1.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

calc_gi | Calculate Genetic Interaction scores
cn_setup | Download and set up DepMap CN
ctrl_genes | Download and set up control genes
delete_annotation | Refresh the annotation files by redownloading them
delete_example_data | Refresh the example data files by redownloading them
encrypt_creds_path | Default creds path
example_data_folder | Get file path to an default credentials RDS
get_example_data | Returns example data for package
get_figshare | Handler function for GET requests from Figshare
gimap_annotate | Annotate gimap data
gimap_filter | A function to run filtering
gimap_normalize | Normalize Log fold changes
gimap_object | Make an empty gimap dataset object
gimap_stats | Do tests -an internal function used by calc_gi() function
key_encrypt_creds_path | Get file path to an key encryption RDS
plot_crispr | Plot CRISPR scores after normalization
plot_exp_v_obs_scatter | Expected vs Observed CRISPR Scatterplot
plot_rank_scatter | Rank plot for target-level GI scores
plot_targets | Target bar plot for CRISPR scores
plot_theme | Standardized plot theme
plot_volcano | Volcano plot for GI scores
qc_cdf | Create a CDF for the pgRNA normalized counts
qc_constructs_countzero_bar | Create a bar graph that shows the number of replicates with a zero count for pgRNA constructs flagged by the zero count filter
qc_cor_heatmap | Create a correlation heatmap for the pgRNA CPMs
qc_filter_plasmid | Create a filter for pgRNAs which have a low log2 CPM value for the plasmid/Day 0 sample/time point
qc_filter_zerocounts | Filter out samples of zero counts Create a filter for pgRNAs which have a raw count of 0 for any sample/time # point
qc_plasmid_histogram | Create a histogram with plasmid log2 CPM values and ascertain a cutoff for low values
qc_sample_hist | Create a histogram for the pgRNA log2 CPMs, faceted by sample
qc_variance_hist | Create a histogram for the variance within replicates for each pgRNA
run_qc | Run Quality Control Checks
save_example_timepoint_data | Set up example count data
save_example_treatment_data | Set up example count data
setup_data | Making a new gimap dataset
supported_cell_lines | List the supported cell lines
tpm_setup | Download and set up DepMap TPM data