Man pages for HenryWard/orthrus
Scoring Combinatorial CRISPR Screens

add_screen	Adds a new screen to a list of screens
add_screens_from_table	Adds a list of screens from a sample table file
call_combn_hits	Call significant responses for scored paired data.
call_condition_hits	Call significant responses for scored data.
check_screen_params	Checks input parameters
chymera_batch_table	Batch table for chymera_paralog
chymera_paralog	Raw reads for paralog screen from CHyMErA paper
chymera_sample_table	Sample table for chymera_paralog
essential_lfc_qc	Computes essential gene recovery AUC.
filter_reads	Filters guides with too few read counts.
load_batch_table	Checks a batch scoring file
normalize_reads	Log-normalizes reads.
normalize_screens	Normalizes reads for given screens
orthrus_wrapper	All-in-one wrapper for Orthrus
plot_combn_gene_residuals	Plot guide-level residuals for a given gene.
plot_combn_residuals	Plot guide-level LFCs for all gene pairs.
plot_combn_response	Plots drug response for scored paired data.
plot_condition_gene_residuals	Plot guide-level residuals for a given gene.
plot_condition_residuals	Plot guide-level residuals for all gene pairs.
plot_condition_response	Plots drug response for scored data.
plot_heatmap	Plots Pearson correlation heatmap.
plot_lfc_qc	Plot replicate comparisons.
plot_reads	Plot read counts.
plot_reads_qc	Plot read counts for a screen.
plot_samples	Plots sample comparisons.
remove_screen	Removes a screen from a list of screens
retrieve_guides_by_gene	Retrieve guide values for gene pairs
retrieve_guides_by_label	Splits guides by type
score_combn_batch	Scores multiple combinatorial screens against derived null...
score_combn_vs_single	Scores conditions against a single control.
score_conditions_batch	Scores multiple conditions against multiple controls
score_conditions_vs_control	Scores conditions against a single control.
split_guides	Splits data into different types of guides
split_guides_by_type	Splits guides by type.
unique_gene_pairs	Get unique gene pairs