API for Katsevich-Lab/sceptre
Analysis of Single-Cell CRISPR Screen Data

Global functions
apply_grouping_to_result	Source code
assign_grnas	Man page Source code
assign_grnas_to_cells	Source code
assign_grnas_to_cells_maximum	Source code
assign_grnas_to_cells_mixture	Source code
assign_grnas_to_cells_thresholding	Source code
auto_compute_cell_covariates	Source code
auto_construct_formula_object	Source code
check_assign_grna_inputs	Source code
check_calibration_check_inputs	Source code
check_discovery_analysis_inputs	Source code
check_import_data_inputs	Source code
check_run_qc_inputs	Source code
check_set_analysis_parameters	Source code
check_sn_tail	Source code
collapse_grna_matrix	Source code
collapse_grna_target_data_frame	Source code
compare_calibration_and_discovery_results	Source code
compute_D_matrix	Source code
compute_calibration_group_size	Source code
compute_cell_covariates	Source code
compute_cell_covariates_cpp	Source code
compute_colwise_max	Source code
compute_empirical_p_value	Source code
compute_genes_within_distance	Source code
compute_n_grnas_per_cell_vector	Source code
compute_n_trt_cells_matrix	Source code
compute_nt_nonzero_matrix_and_n_ok_pairs_v3	Source code
compute_pairwise_qc_information	Source code
compute_precomputation_pieces	Source code
compute_qc_metrics	Source code
compute_tolerance_cpp	Source code
construct_cis_pairs	Man page Source code
construct_data_frame_v2	Source code
construct_negative_control_pairs_v2	Source code
construct_positive_control_pairs	Man page Source code
construct_trans_pairs	Man page Source code
convert_covariate_df_to_design_matrix	Source code
convert_pointer_to_index_vector_v2	Source code
create_csc_matrix	Source code
crt_glm_factored_out	Source code
crt_index_sampler	Source code
crt_index_sampler_fast	Source code
determine_cells_to_retain	Source code
determine_grnas_in_use	Source code
discovery_ntcells_crt	Source code
discovery_ntcells_perm_test	Source code
downsample_result_data_frame	Source code
estimate_theta	Source code
fisher_yates_samlper	Source code
fit_and_evaluate_skew_normal	Source code
fit_skew_normal_funct	Source code
gene_position_data_frame_grch37	Man page
gene_position_data_frame_grch38	Man page
get_cell_covariates	Man page Source code
get_grna_assignments	Man page Source code
get_grna_matrix	Man page Source code
get_id_from_idx	Source code
get_id_vect	Source code
get_idx_vector_calibration_check	Source code
get_idx_vector_discovery_analysis	Source code
get_idx_vector_factory	Source code
get_log_dir	Source code
get_mtx_metadata	Source code
get_my_theme	Source code
get_random_starting_guesses	Source code
get_response_matrix	Man page Source code
get_result	Man page Source code
get_synthetic_permutation_idxs	Source code
get_undercover_group_names	Source code
hybrid_fisher_iwor_sampler	Source code
import_data	Man page Source code
import_data_from_cellranger	Man page Source code
import_data_from_cellranger_memory	Source code
import_data_from_cellranger_use_ondisc	Source code
import_data_from_parse	Man page Source code
import_data_memory	Source code
import_data_use_ondisc	Source code
increment_matrix	Source code
increment_vector	Source code
init_sceptre_object	Source code
iterate_over_combinations	Source code
load_csr_row	Source code
load_row	Source code
make_volcano_plot	Source code
obtain_em_assignments	Source code
obtain_pointer_vector	Source code
partition_response_ids	Source code
perform_grna_precomputation	Source code
perform_response_precomputation	Source code
perform_status_check_and_update	Source code
perm_test_glm_factored_out	Source code
plot,sceptre_object-method	Man page
plot_assign_grnas	Man page Source code
plot_cellwise_qc	Source code
plot_covariates	Man page Source code
plot_grna_count_distributions	Man page Source code
plot_pairwise_qc	Source code
plot_response_grna_target_pair	Man page Source code
plot_run_calibration_check	Man page Source code
plot_run_discovery_analysis	Man page Source code
plot_run_power_check	Man page Source code
plot_run_qc	Man page Source code
print,sceptre_object-method	Man page
print_synth_idx_list_row	Source code
process_calibration_result	Source code
process_covariates_and_matrices	Source code
process_discovery_result	Source code
process_initial_assignment_list	Source code
read_ondisc_backed_sceptre_object	Man page Source code
revlog_trans	Source code
run_calibration_check	Man page Source code
run_calibration_check_pt_1	Source code
run_calibration_check_pt_2	Source code
run_crt_in_memory_v2	Source code
run_discovery_analysis	Man page Source code
run_low_level_test_full_v4	Source code
run_perm_test_in_memory	Source code
run_power_check	Man page Source code
run_qc	Man page Source code
run_qc_pt_1	Source code
run_qc_pt_2	Source code
run_reduced_em_algo_cpp	Source code
run_sceptre_analysis_high_level	Source code
sample_combinations_v2	Source code
sample_undercover_pairs_v2	Source code
sceptre	Man page
sceptre-package	Man page
set_analysis_parameters	Man page Source code
set_colnames	Source code
set_grna_matrix	Source code
set_matrix_accessibility	Source code
set_response_matrix	Source code
set_rownames	Source code
skip_assign_grnas_and_run_qc	Source code
stat_qq_band	Source code
stat_qq_points	Source code
synth_idx_list_to_matrix	Source code
synth_idx_list_to_r_list	Source code
test	Source code
threshold_count_matrix	Source code
update_dfs_based_on_grouping_strategy	Source code
update_grna_assignments_given_qc	Source code
update_indiv_grna_assignments_for_nt_cells	Source code
write_matrices_to_disk	Source code
write_ondisc_backed_sceptre_object	Man page Source code
write_outputs_to_directory	Man page Source code
write_vector	Source code