Index

A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y

A

ADAF, [1]
add_pvalues_correction() (ANOVA method)
anaconda
analyse() (GDSC method)
annotate_all() (GDSC1000 method)
anova
ANOVA (class in gdsctools.anova)
anova_all() (ANOVA method)
anova_one_drug() (ANOVA method)
anova_one_drug_one_feature() (ANOVA method)
anova_one_drug_one_feature_custom() (ANOVA method)
ANOVAReport (class in gdsctools.anova_report)
ANOVAResults (class in gdsctools.anova_results)
ANOVASettings (class in gdsctools.settings)
astype() (ANOVAResults method)
authors (Data attribute)

B

barplot_effect_size() (ANOVAResults method)
BaseModels (class in gdsctools.models)
beeswarm() (BoxSwarm method)
boxplot() (Regression method)
boxplot_association() (BoxPlots method)
boxplot_pancan() (BoxPlots method)
BoxPlots (class in gdsctools.boxplots)
BoxPlotsJS (class in gdsctools.boxplots)
BoxSwarm (class in gdsctools.boxswarm)
boxswarm() (in module gdsctools.boxswarm)

C

cell lines
check() (ANOVASettings method)
(DrugDecode method)
(Reader method)
check_randomness() (Regression method)
ChemSpiderSearch (class in gdsctools.drugs)
cleanup() (IC50Cluster method)
CLI
cluster() (IC50Cluster method)
cohens
cohens() (in module gdsctools.stats)
colnames (GenomicFeatures attribute)
companies (DrugDecode attribute)
(GDSC attribute)
compress_identical_features() (GenomicFeatures method)
copy() (ANOVAResults method)
(IC50 method)
COSMIC
cosmic_name (IC50 attribute)
COSMICFetcher (class in gdsctools.cosmictools)
cosmicIds (BaseModels attribute)
COSMICInfo (class in gdsctools.cosmictools)
create_data_packages_for_companies() (GDSC method)
create_html_associations() (ANOVAReport method)
create_html_drug() (RegressionReport method)
create_html_drugs() (ANOVAReport method)
create_html_features() (ANOVAReport method)
create_html_main() (ANOVAReport method)
(RegressionReport method)
create_html_manova() (ANOVAReport method)
create_html_pages() (ANOVAReport method)
create_report() (ReportMain method)
create_summary_pages() (GDSC method)
CSV

D

Data (class in gdsctools.datasets)
dendogram_coefficients() (Regression method)
description (Data attribute)
df (ANOVAResults attribute)
(COSMICInfo attribute)
diagnostics() (ANOVAReport method)
(BaseModels method)
directory (BoxPlots attribute)
(Savefig attribute)
download_data() (GDSC1000 method)
drop_drugs() (IC50 method)
drop_tissue_in() (GenomicFeatures method)
drug
drug_annotations() (DrugDecode method)
drug_name_to_int() (IC50 method)
drug_names (DrugDecode attribute)
drug_summary() (ANOVAReport method)
drug_targets (DrugDecode attribute)
DrugDecode (class in gdsctools.readers)
drugIds (ANOVAResults attribute)
(BaseModels attribute)
(DrugDecode attribute)
(IC50 attribute)
duplicated (IC50Cluster attribute)

E

EC50
ec50
enetpath_vs_enet() (GDSCElasticNet method)
estimate_pi0() (QValue method)

F

FDR
feature_names (BaseModels attribute)
feature_summary() (ANOVAReport method)
features (GenomicFeatures attribute)
filename (Data attribute)
fill_media_factor() (GenomicFeatures method)
filling_chembl_pubchem_using_unichem() (ChemSpiderSearch method)
filter_by_alteration_type() (GDSC1000 method)
filter_by_cell_line() (GDSC1000 method)
filter_by_cosmic_id() (GDSC1000 method)
filter_by_cosmic_list() (OmniBEMBuilder method)
filter_by_gene() (GDSC1000 method)
filter_by_gene_list() (OmniBEMBuilder method)
filter_by_recurrence() (GDSC1000 method)
filter_by_sample_list() (OmniBEMBuilder method)
filter_by_tissue_list() (OmniBEMBuilder method)
filter_by_tissue_type() (GDSC1000 method)
filter_by_type_list() (OmniBEMBuilder method)
find_chembl_ids() (ChemSpiderSearch method)
fit() (Regression method)
fontsize (BoxPlots attribute)

G

GDSC (class in gdsctools.gdsc)
GDSC1000 (class in gdsctools.gdsc1000)
GDSCElasticNet (class in gdsctools.regression)
GDSCLasso (class in gdsctools.regression)
GDSCRidge (class in gdsctools.regression)
gdsctools.anova (module)
gdsctools.anova_report (module)
gdsctools.anova_results (module)
gdsctools.boxplots (module)
gdsctools.boxswarm (module)
gdsctools.cosmictools (module)
gdsctools.datasets (module)
gdsctools.drugs (module)
gdsctools.errors (module)
gdsctools.gdsc (module)
gdsctools.gdsc1000 (module)
gdsctools.logistics (module)
gdsctools.models (module)
gdsctools.omnibem (module)
gdsctools.qvalue (module)
gdsctools.readers (module)
gdsctools.regression_report (module)
gdsctools.report (module)
gdsctools.settings (module)
gdsctools.stats (module)
gdsctools.tissues (module)
gdsctools.tools (module)
gdsctools.volcano (module)
gdsctools_anova
GDSCToolsDuplicatedDrugError
GDSCToolsError
genomic features
GenomicFeatures (class in gdsctools.readers)
get() (COSMICInfo method)
get_best_model() (Regression method)
get_chemspider_ids() (ChemSpiderSearch method)
get_cna_info() (GDSC1000 method)
get_corrected_pvalues() (MultipleTesting method)
get_drug_id() (in module gdsctools.tools)
get_drug_summary_data() (ANOVAReport method)
get_fdr_ypos() (VolcanoANOVAJS method)
get_feature_summary_data() (ANOVAReport method)
get_genomic_features() (OmniBEMBuilder method)
get_genomic_info() (GDSC1000 method)
get_html_association() (BoxPlotsJS method)
get_html_media() (BoxPlotsJS method)
get_html_msi() (BoxPlotsJS method)
get_html_table() (ANOVAResults method)
get_html_tissue() (BoxPlotsJS method)
get_ic50() (IC50 method)
get_info() (DrugDecode method)
get_methylation_info() (GDSC1000 method)
get_mobem() (OmniBEMBuilder method)
get_model() (GDSCElasticNet method)
(GDSCLasso method)
(GDSCRidge method)
get_name() (DrugDecode method)
get_public_and_one_company() (DrugDecode method)
get_significant_genes() (OmniBEMBuilder method)
get_significant_hits() (ANOVAReport method)
get_significant_set() (ANOVAReport method)
get_snr() (LogisticMatchedFiltering method)
get_target() (DrugDecode method)
get_TCGA() (GenomicFeatures method)

H

header (Reader attribute)
help
hist() (IC50 method)

I

IC50, [1], [2]
ic50
IC50 (class in gdsctools.readers)
IC50Cluster (class in gdsctools.gdsc)
init() (BaseModels method)
installation, [1]
IPython, [1]
is_public() (DrugDecode method)

K

keep_tissue_in() (GenomicFeatures method)

L

load_data() (GDSC1000 method)
location (Data attribute)
Logistic (class in gdsctools.logistics)
LogisticMatchedFiltering (class in gdsctools.logistics)
lw (BoxPlots attribute)

M

make_matrix() (GDSC1000 method)
mapping (ANOVAResults attribute)
MEDIA
method (MultipleTesting attribute)
MoBEM
MSI
multiple testing
MultipleTesting (class in gdsctools.stats)

N

N (Logistic attribute)
(LogisticMatchedFiltering attribute)
n_celllines (ANOVAReport attribute)
n_drugs (ANOVAReport attribute)
n_tests (ANOVAReport attribute)

O

objective_function() (LogisticMatchedFiltering method)
ODAF, [1]
ODOF, [1]
odof (BoxPlots attribute)
OLS
OmniBEMBuilder (class in gdsctools.omnibem)
on_web() (COSMICInfo method)
onweb() (ANOVAReport method)
optimise() (LogisticMatchedFiltering method)

P

PANCAN
pip
plot() (BoxSwarm method)
(GenomicFeatures method)
(Logistic method)
(LogisticMatchedFiltering method)
plot_alterations_per_cellline() (OmniBEMBuilder method)
plot_cindex() (GDSCElasticNet method)
plot_comparison() (MultipleTesting method)
plot_ic50_count() (IC50 method)
plot_importance() (Regression method)
plot_number_alteration_by_tissue() (OmniBEMBuilder method)
plot_weight() (Regression method)

Q

QValue (class in gdsctools.qvalue)
qvalue() (QValue method)

R

read_csv() (ANOVAResults method)
read_data() (Reader method)
read_drug_decode() (BaseModels method)
read_settings() (BaseModels method)
Reader (class in gdsctools.readers)
Regression (class in gdsctools.regression)
RegressionReport (class in gdsctools.regression_report)
render_all() (VolcanoANOVAJS method)
render_drug() (VolcanoANOVAJS method)
render_feature() (VolcanoANOVAJS method)
ReportMain (class in gdsctools.report)
reset_buffer() (ANOVA method)
reset_genomic_data() (GDSC1000 method)
runCV() (Regression method)

S

savefig (BoxPlots attribute)
Savefig (class in gdsctools.tools)
savefig() (Savefig method)
(VolcanoANOVA method)
scale (Logistic attribute)
(LogisticMatchedFiltering attribute)
scan() (LogisticMatchedFiltering method)
search_from_smile_inchembl() (ChemSpiderSearch method)
search_in_chemspider() (ChemSpiderSearch method)
selector() (VolcanoANOVA method)
set_cancer_type() (BaseModels method)
set_noisy_data() (LogisticMatchedFiltering method)
settings (BaseModels attribute)
shell
shift (GenomicFeatures attribute)
show() (ReportMain method)
signed effects
signed_effects() (in module gdsctools.stats)
standalone

T

TCGA
(class in gdsctools.tissues)
tcga (GDSC attribute)
TCGA_GDSC1000 (in module gdsctools.tissues)
Terminal
Tissues (class in gdsctools.tissues)
tissues (GenomicFeatures attribute)
to_cluster (IC50Cluster attribute)
to_csv() (ANOVAResults method)
(Reader method)
to_html() (ANOVASettings method)
TSV
tune_alpha() (Regression method)

U

unique_tissues (GenomicFeatures attribute)

V

valid_methods (MultipleTesting attribute)
volcano
volcano() (ANOVAResults method)
volcano_plot_all() (VolcanoANOVA method)
volcano_plot_all_drugs() (VolcanoANOVA method)
volcano_plot_all_features() (VolcanoANOVA method)
volcano_plot_one_drug() (VolcanoANOVA method)
volcano_plot_one_feature() (VolcanoANOVA method)
VolcanoANOVA (class in gdsctools.volcano)
VolcanoANOVAJS (class in gdsctools.volcano)

W

warnings

X

X (Logistic attribute)
(LogisticMatchedFiltering attribute)
xmax (Logistic attribute)
xmid (LogisticMatchedFiltering attribute)
xmin (Logistic attribute)

Y

Y (Logistic attribute)