Package index • gimap

All functions
`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
`setup_data()`	Making a new gimap dataset
`supported_cell_lines()`	List the supported cell lines
`tpm_setup()`	Download and set up DepMap TPM data

Reference

All functions