Index

Symbols

--counts phippery-about-feature command line option --counts_matrix phippery-load-from-csv command line option --dimension phippery-about-feature command line option phippery-query-expression command line option --distribution phippery-about-feature command line option --output phippery-load-from-csv command line option phippery-merge command line option phippery-query-expression command line option phippery-query-table command line option phippery-to-tall-csv command line option --output-prefix phippery-to-wide-csv command line option --peptide_table phippery-load-from-csv command line option --sample_table phippery-load-from-csv command line option

--verbose phippery-about command line option -c phippery-load-from-csv command line option -d phippery-about-feature command line option phippery-query-expression command line option -o phippery-load-from-csv command line option phippery-merge command line option phippery-query-expression command line option phippery-query-table command line option phippery-to-tall-csv command line option phippery-to-wide-csv command line option -p phippery-load-from-csv command line option -s phippery-load-from-csv command line option -v phippery-about command line option

A

add_enrichment_layer_from_array() (in module phippery.utils)

C

collapse_groups() (in module phippery.utils) collapse_peptide_groups() (in module phippery.utils) collapse_sample_groups() (in module phippery.utils)

collect_counts() (in module phippery.utils) compute_sim_score() (in module phippery.escprof) counts_per_million() (in module phippery.normalize)

D

dataset_from_csv() (in module phippery.utils) DATASETS phippery-merge command line option

differential_selection_sample_groups() (in module phippery.normalize) differential_selection_wt_mut() (in module phippery.normalize) ds_query() (in module phippery.utils) dump() (in module phippery.utils)

E

eigenassay_projections() (in module phippery.eigen) enrichment() (in module phippery.normalize) EXPRESSION phippery-query-expression command line option

EXPRESSION_TABLE phippery-query-table command line option

F

FEATURE phippery-about-feature command line option FILENAME phippery-about command line option phippery-about-feature command line option phippery-query-expression command line option phippery-query-table command line option phippery-to-tall-csv command line option phippery-to-wide-csv command line option

G

gamma_poisson_model() (in module phippery.modeling) get_annotation_table() (in module phippery.utils)

get_cost_matrix() (in module phippery.escprof) get_loc_esc_distr() (in module phippery.escprof)

I

id_coordinate_from_query_df() (in module phippery.utils)

id_query() (in module phippery.utils) iter_groups() (in module phippery.utils)

L

load() (in module phippery.utils)

loc_sim_score() (in module phippery.escprof)

M

module phippery.eigen phippery.escprof phippery.modeling phippery.normalize phippery.utils

P

phippery-about command line option --verbose -v FILENAME phippery-about-feature command line option --counts --dimension --distribution -d FEATURE FILENAME phippery-load-from-csv command line option --counts_matrix --output --peptide_table --sample_table -c -o -p -s phippery-merge command line option --output -o DATASETS phippery-query-expression command line option --dimension --output -d -o EXPRESSION FILENAME

phippery-query-table command line option --output -o EXPRESSION_TABLE FILENAME phippery-to-tall-csv command line option --output -o FILENAME phippery-to-wide-csv command line option --output-prefix -o FILENAME phippery.eigen module phippery.escprof module phippery.modeling module phippery.normalize module phippery.utils module

R

rank_data() (in module phippery.normalize)

region_sim_score() (in module phippery.escprof)

S

size_factors() (in module phippery.normalize) standardized_enrichment() (in module phippery.normalize)

stitch_dataset() (in module phippery.utils) svd_aa_loc() (in module phippery.normalize) svd_rank_reduction() (in module phippery.normalize)

T

to_tall() (in module phippery.utils)

to_wide() (in module phippery.utils) to_wide_csv() (in module phippery.utils)

Y

yield_tall() (in module phippery.utils)

Z

zscore() (in module phippery.modeling)