Index

A

accessionNumber (bioscience.base.models.NCBIDataset property) annotations (bioscience.base.models.Dataset property)

apiKey (bioscience.base.models.NCBIClient property) ari() (in module bioscience.stats.correlation.mixed.ARI)

B

baseUrl (bioscience.base.models.NCBIClient property) bcca() (in module bioscience.dataMining.biclustering.Biclustering) bibit() (in module bioscience.dataMining.biclustering.Biclustering) Bicluster (class in bioscience.base.models) BiclusteringModel (class in bioscience.base.models) binarize() (in module bioscience.preprocess.Binarization) binarizeLevels() (in module bioscience.preprocess.Binarization) bioProject (bioscience.base.models.NCBIDataset property) bioscience.base.files module bioscience.base.models module bioscience.dataMining.biclustering.BiBit module bioscience.dataMining.biclustering.Biclustering module bioscience.preprocess.Binarization module bioscience.preprocess.RnaSeq module bioscience.preprocess.Standard module bioscience.stats.correlation.continuous.DistCorr module bioscience.stats.correlation.continuous.Median module bioscience.stats.correlation.continuous.Pearson module bioscience.stats.correlation.continuous.Quadrant module

bioscience.stats.correlation.dichotomic.Log_odds module bioscience.stats.correlation.dichotomic.MCC module bioscience.stats.correlation.dichotomic.PBC module bioscience.stats.correlation.mixed.ARI module bioscience.stats.correlation.mixed.CC module bioscience.stats.correlation.mixed.MI module bioscience.stats.correlation.mixed.NMI module bioscience.stats.correlation.ordinal.HoeffdingsD module bioscience.stats.correlation.ordinal.Kendall module bioscience.stats.correlation.ordinal.Spearman module bioscience.stats.distance.Cosine module bioscience.stats.distance.Euclidean module bioscience.stats.distance.Jaccard module bioscience.stats.distance.Manhattan module bioscience.stats.distance.WeightedJaccard module

C

cc() (in module bioscience.stats.correlation.mixed.CC) cols (bioscience.base.models.Bicluster property) columnsNames (bioscience.base.models.Dataset property)

CorrelationModel (class in bioscience.base.models) cos() (in module bioscience.stats.distance.Cosine) cpm() (in module bioscience.preprocess.RnaSeq) cut (bioscience.base.models.Dataset property)

D

data (bioscience.base.models.Bicluster property) (bioscience.base.models.Dataset property) Dataset (class in bioscience.base.models)

deseq2Norm() (in module bioscience.preprocess.RnaSeq) discretize() (in module bioscience.preprocess.Standard) distcorr() (in module bioscience.stats.correlation.continuous.DistCorr)

E

euclidean() (in module bioscience.stats.distance.Euclidean)

executionTime (bioscience.base.models.BiclusteringModel property) (bioscience.base.models.CorrelationModel property)

F

fpkm() (in module bioscience.preprocess.RnaSeq)

fullInfo() (bioscience.base.models.NCBIDataset method)

G

gdstype (bioscience.base.models.NCBIDataset property) geneInteractionsIndex (bioscience.base.models.CorrelationModel property) geneNames (bioscience.base.models.Dataset property)

getIdsByGeo() (bioscience.base.models.NCBIClient method) getSummaryById() (bioscience.base.models.NCBIClient method) gpl (bioscience.base.models.NCBIDataset property) gse (bioscience.base.models.NCBIDataset property)

H

hoeffdingsD() (in module bioscience.stats.correlation.ordinal.HoeffdingsD)

I

idDB (bioscience.base.models.NCBIClient property)

J

jaccard() (in module bioscience.stats.distance.Jaccard)

K

kendall() (in module bioscience.stats.correlation.ordinal.Kendall)

L

lengths (bioscience.base.models.Dataset property) link (bioscience.base.models.NCBIDataset property)

load() (in module bioscience.base.files) log_odds() (in module bioscience.stats.correlation.dichotomic.Log_odds)

M

manhattan() (in module bioscience.stats.distance.Manhattan) mcc() (in module bioscience.stats.correlation.dichotomic.MCC) measure (bioscience.base.models.Validation property) median() (in module bioscience.stats.correlation.continuous.Median) mi() (in module bioscience.stats.correlation.mixed.MI) module bioscience.base.files bioscience.base.models bioscience.dataMining.biclustering.BiBit bioscience.dataMining.biclustering.Biclustering bioscience.preprocess.Binarization bioscience.preprocess.RnaSeq bioscience.preprocess.Standard bioscience.stats.correlation.continuous.DistCorr bioscience.stats.correlation.continuous.Median bioscience.stats.correlation.continuous.Pearson bioscience.stats.correlation.continuous.Quadrant bioscience.stats.correlation.dichotomic.Log_odds bioscience.stats.correlation.dichotomic.MCC bioscience.stats.correlation.dichotomic.PBC bioscience.stats.correlation.mixed.ARI bioscience.stats.correlation.mixed.CC bioscience.stats.correlation.mixed.MI bioscience.stats.correlation.mixed.NMI bioscience.stats.correlation.ordinal.HoeffdingsD bioscience.stats.correlation.ordinal.Kendall bioscience.stats.correlation.ordinal.Spearman bioscience.stats.distance.Cosine bioscience.stats.distance.Euclidean bioscience.stats.distance.Jaccard bioscience.stats.distance.Manhattan bioscience.stats.distance.WeightedJaccard

N

name (bioscience.base.models.CorrelationModel property) NCBIClient (class in bioscience.base.models) NCBIDataset (class in bioscience.base.models)

nmi() (in module bioscience.stats.correlation.mixed.NMI) normalDistributionQuantile() (in module bioscience.preprocess.Standard) nSamples (bioscience.base.models.NCBIDataset property)

O

original (bioscience.base.models.Dataset property)

outliers() (in module bioscience.preprocess.Standard)

P

pbc() (in module bioscience.stats.correlation.dichotomic.PBC)

pearson() (in module bioscience.stats.correlation.continuous.Pearson) processBiBit() (in module bioscience.dataMining.biclustering.BiBit)

Q

q() (in module bioscience.stats.correlation.continuous.Quadrant)

R

results (bioscience.base.models.BiclusteringModel property) (bioscience.base.models.CorrelationModel property)

rows (bioscience.base.models.Bicluster property)

S

samples (bioscience.base.models.NCBIDataset property) saveBinaryDatasets() (in module bioscience.base.files) saveGenes() (in module bioscience.base.files) saveResults() (in module bioscience.base.files) saveResultsIndex() (in module bioscience.base.files) scale() (in module bioscience.preprocess.Standard)

sizeBicluster() (bioscience.base.models.Bicluster method) sort() (bioscience.base.models.Bicluster method) spearman() (in module bioscience.stats.correlation.ordinal.Spearman) standardize() (in module bioscience.preprocess.Standard) summary (bioscience.base.models.NCBIDataset property) suppfile (bioscience.base.models.NCBIDataset property)

T

taxonomy (bioscience.base.models.NCBIDataset property) threadsPerDevice_64() (in module bioscience.dataMining.biclustering.BiBit)

title (bioscience.base.models.NCBIDataset property) tpm() (in module bioscience.preprocess.RnaSeq)

V

Validation (class in bioscience.base.models)

validations (bioscience.base.models.Bicluster property) value (bioscience.base.models.Validation property)

W

weightedJaccard() (in module bioscience.stats.distance.WeightedJaccard)