Index

_

__init__() (pyrnaither.logging.logger.ColorFormatter method), [1] (pyrnaither.main.PyRNAither method)

B

b_score() (in module pyrnaither.normalization.normalizer), [1]

C

closest_to_zero() (in module pyrnaither.utils.utilities), [1] ColorFormatter (class in pyrnaither.logging.logger), [1] compare_hits() (in module pyrnaither.stats.stattests), [1] compare_replica_plates() (in module pyrnaither.stats.qc), [1] compare_replicate_sd() (in module pyrnaither.stats.qc), [1] compare_replicate_sd_per_screen() (in module pyrnaither.stats.qc), [1]

compare_replicates() (in module pyrnaither.stats.qc), [1] control_density() (in module pyrnaither.stats.qc), [1] control_density_per_plate() (in module pyrnaither.stats.qc), [1] control_density_per_screen() (in module pyrnaither.stats.qc), [1] control_norm() (in module pyrnaither.normalization.normalizer), [1] create_subset() (in module pyrnaither.utils.utilities), [1]

D

discard_labtek() (in module pyrnaither.stats.qc), [1] discard_wells() (in module pyrnaither.stats.qc), [1] div_norm() (in module pyrnaither.normalization.normalizer), [1]

divide_channels() (in module pyrnaither.utils.utilities), [1] dr_qual_control() (in module pyrnaither.stats.qc), [1] dynamic_range() (in module pyrnaither.stats.qc), [1]

E

erase_dataset_column() (in module pyrnaither.utils.utilities), [1]

F

find_replicates() (in module pyrnaither.utils.utilities), [1]

format() (pyrnaither.logging.logger.ColorFormatter method), [1] furthest_from_zero() (in module pyrnaither.utils.utilities), [1]

G

generate_dataset_file() (in module pyrnaither.data.datasets), [1] generate_replicate_mat() (in module pyrnaither.utils.utilities), [1]

generate_replicate_matrix() (in module pyrnaither.stats.qc_todo), [1] generate_replicate_matrix_no_filter() (in module pyrnaither.utils.utilities), [1] get_complementary_color() (in module pyrnaither.visualization.visualizer), [1]

H

handle_exception() (in module pyrnaither.logging.logger), [1] hit_selection_pval() (in module pyrnaither.stats.stattests), [1]

hit_selection_zscore() (in module pyrnaither.stats.stattests), [1] hit_selection_zscore_pval() (in module pyrnaither.stats.stattests), [1]

I

incorporate_pval_vec() (in module pyrnaither.stats.stattests), [1]

index_subset() (in module pyrnaither.utils.utilities), [1]

L

load_data() (pyrnaither.main.PyRNAither method)

lowess_norm() (in module pyrnaither.normalization.normalizer), [1]

M

main() (in module pyrnaither.main) make_boxplot_4_plate_type() (in module pyrnaither.stats.qc), [1] make_boxplot_controls() (in module pyrnaither.stats.qc), [1] make_boxplot_controls_per_plate() (in module pyrnaither.stats.qc), [1] make_boxplot_controls_per_screen() (in module pyrnaither.stats.qc), [1] make_boxplot_per_plate() (in module pyrnaither.stats.qc), [1] make_boxplot_per_screen() (in module pyrnaither.stats.qc), [1] mann_whitney() (in module pyrnaither.stats.stattests), [1] med_abs_dev() (in module pyrnaither.normalization.normalizer), [1] median_polish() (in module pyrnaither.normalization.normalizer), [1] module pyrnaither pyrnaither.data, [1] pyrnaither.data.datasets, [1] pyrnaither.logging pyrnaither.logging.logger, [1] pyrnaither.main pyrnaither.normalization, [1] pyrnaither.normalization.normalizer, [1] pyrnaither.pipeline, [1] pyrnaither.pipeline.workflow, [1] pyrnaither.stats, [1] pyrnaither.stats.qc, [1] pyrnaither.stats.qc_todo, [1] pyrnaither.stats.stattests, [1] pyrnaither.stats.stattests_todo, [1] pyrnaither.utils, [1] pyrnaither.utils.utilities, [1] pyrnaither.visualization, [1] pyrnaither.visualization.visualizer, [1]

mult_test_adjust() (in module pyrnaither.stats.stattests), [1]

N

normalize() (pyrnaither.main.PyRNAither method)

num_cell_qual_control() (in module pyrnaither.stats.qc), [1]

O

order_gene_ids() (in module pyrnaither.stats.stattests_todo), [1] (in module pyrnaither.utils.utilities), [1]

P

parse_arguments() (in module pyrnaither.main) PdfPages() (in module pyrnaither.stats.qc_todo), [1] perc_cell_qual_control() (in module pyrnaither.stats.qc), [1] plot_96_well_plate_with_intensity() (in module pyrnaither.visualization.visualizer), [1] plot_control_histo() (in module pyrnaither.stats.qc), [1] plot_control_histo_per_plate() (in module pyrnaither.stats.qc), [1] plot_histo() (in module pyrnaither.stats.qc), [1] plot_histo_per_plate() (in module pyrnaither.stats.qc), [1] plot_histo_per_screen() (in module pyrnaither.stats.qc), [1] plot_qq() (in module pyrnaither.stats.qc), [1] plot_qq_per_plate() (in module pyrnaither.stats.qc), [1] plot_qq_per_screen() (in module pyrnaither.stats.qc), [1] pyrnaither module PyRNAither (class in pyrnaither.main) pyrnaither.data module, [1] pyrnaither.data.datasets module, [1] pyrnaither.logging module pyrnaither.logging.logger module, [1] pyrnaither.main module

pyrnaither.normalization module, [1] pyrnaither.normalization.normalizer module, [1] pyrnaither.pipeline module, [1] pyrnaither.pipeline.workflow module, [1] pyrnaither.stats module, [1] pyrnaither.stats.qc module, [1] pyrnaither.stats.qc_todo module, [1] pyrnaither.stats.stattests module, [1] pyrnaither.stats.stattests_todo module, [1] pyrnaither.utils module, [1] pyrnaither.utils.utilities module, [1] pyrnaither.visualization module, [1] pyrnaither.visualization.visualizer module, [1]

Q

quantile_normalization() (in module pyrnaither.normalization.normalizer), [1]

R

rank_product() (in module pyrnaither.stats.stattests), [1] read_dataset_with_header() (in module pyrnaither.stats.qc), [1] replicates_cv() (in module pyrnaither.stats.qc), [1]

replicates_spearman_cor() (in module pyrnaither.stats.qc), [1] rms() (in module pyrnaither.utils.utilities), [1] run_quality_control() (pyrnaither.main.PyRNAither method)

S

save_dataset() (in module pyrnaither.normalization.normalizer), [1] save_old_intensity_columns() (in module pyrnaither.normalization.normalizer), [1] setup_logger() (in module pyrnaither.logging.logger), [1] snr_qual_control() (in module pyrnaither.stats.qc), [1] spatial_distrib() (in module pyrnaither.stats.qc), [1] (in module pyrnaither.visualization.visualizer), [1]

spatial_distrib_hits() (in module pyrnaither.stats.stattests), [1] subtract_background() (in module pyrnaither.normalization.normalizer), [1] sum_channels() (in module pyrnaither.utils.utilities), [1] summarize_reps() (in module pyrnaither.utils.utilities), [1] summarize_reps_no_filtering() (in module pyrnaither.stats.qc_todo), [1]

T

t_test() (in module pyrnaither.stats.stattests), [1]

trim_avg() (in module pyrnaither.utils.utilities), [1]

V

var_adjust() (in module pyrnaither.normalization.normalizer), [1] venn_diag() (in module pyrnaither.stats.stattests), [1]

visualize() (pyrnaither.main.PyRNAither method) volcano_plot() (in module pyrnaither.stats.stattests), [1]

Z

z_prime() (in module pyrnaither.stats.qc), [1] z_score() (in module pyrnaither.normalization.normalizer), [1]

z_score_per_screen() (in module pyrnaither.normalization.normalizer), [1] zprime_qual_control() (in module pyrnaither.stats.qc), [1]