Reference

All functions

calc_gi()

Calculate Genetic Interaction scores

example_data_folder()

Get file path to an default credentials RDS

get_example_data()

Returns example data for package

gimap_annotate()

Annotate gimap data

gimap_filter()

A function to run filtering

gimap_normalize()

Normalize Log fold changes

gimap_rep_stats()

Do tests for each replicate –an internal function used by calc_gi() function

plot_crispr()

Plot CRISPR scores after normalization

plot_exp_v_obs_scatter()

Plots for Genetic interactions

plot_rank_scatter()

Rank plot for target-level GI scores

plot_targets_bar()

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()

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