GDSCTools
latest
1. Installation
2. Quick Start
3. Data Format and Readers
4. ANOVA analysis (introduction)
5. The ANOVA analysis in details
6. HTML report
7. Data Packages
8. OmniBEM Builder
9. Regression analysis
10. Notebooks
11. Standalone application
12. Gallery / Examples
13. Reproducibility
14. References
15. For developers
ChangeLog
FAQS
Glossary
GDSCTools
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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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_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)
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