Man pages for gimap
Calculate Genetic Interactions for Paired CRISPR Targets
| calc_gi | Calculate Genetic Interaction scores |
| check_internet_available | Check if internet/URL is available |
| 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 |
| figshare_manual_download_message | Build manual download instructions for Figshare files |
| get_example_data | Returns example data for package |
| get_figshare | Handler function for GET requests from Figshare |
| gimap_annotate | Annotate gimap data |
| gimap_data_dir | Resolve and create data directory |
| 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 |
| normalize_depmap_metadata | Normalize DepMap metadata for downstream joins |
| pipe | Pipe operator |
| 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... |
| 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... |
| qc_filter_zerocounts | Filter out samples of zero counts Create a filter for pgRNAs... |
| qc_plasmid_histogram | Create a histogram with plasmid log2 CPM values and ascertain... |
| 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... |
| resolve_example_data_dir | Default directory for [get_example_data()] and related... |
| 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 |
