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     Delete cached Figshare example files
encrypt_creds_path      Default creds path
example_data_folder     Folder used for Figshare example data
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
