Index

_

__init__() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) (inmoose.edgepy.DGEList method) (inmoose.utils.Factor method)

A

addPriorCount() (in module inmoose.edgepy) adjustedProfileLik() (in module inmoose.edgepy)

airway() (in module inmoose.data.airway) AveLogCPM (inmoose.edgepy.DGEList attribute) aveLogCPM() (in module inmoose.edgepy)

C

collapseReplicates() (in module inmoose.deseq2) common_dispersion (inmoose.edgepy.DGEList attribute)

counts (inmoose.edgepy.DGEList attribute) counts() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method)

D

DESeq() (in module inmoose.deseq2) DESeqDataSet (class in inmoose.deseq2.DESeqDataSet) DESeqResults (class in inmoose.deseq2.results) design (inmoose.deseq2.DESeqDataSet.DESeqDataSet property) designAsFactor() (in module inmoose.edgepy)

DGEList (class in inmoose.edgepy) dispCoxReid() (in module inmoose.edgepy) dispCoxReidInterpolateTagwise() (in module inmoose.edgepy) dispersionFunction (inmoose.deseq2.DESeqDataSet.DESeqDataSet property) dispersions (inmoose.deseq2.DESeqDataSet.DESeqDataSet property)

E

estimateBetaPriorVar() (in module inmoose.deseq2) estimateDispersions() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) estimateDispersionsFit() (in module inmoose.deseq2) estimateDispersionsGeneEst() (in module inmoose.deseq2) estimateDispersionsMAP() (in module inmoose.deseq2)

estimateDispersionsPriorVar() (in module inmoose.deseq2) estimateGLMCommonDisp() (in module inmoose.edgepy) estimateGLMTagwiseDisp() (in module inmoose.edgepy) estimateSizeFactors() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) estimateSizeFactorsForMatrix() (in module inmoose.deseq2)

F

Factor (class in inmoose.utils)

filtered_p() (in module inmoose.deseq2.results)

G

genes (inmoose.edgepy.DGEList attribute)

glmFit() (in module inmoose.edgepy)

M

makeExampleDESeqDataSet() (in module inmoose.deseq2) mglmLevenberg() (in module inmoose.edgepy)

mglmOneGroup() (in module inmoose.edgepy) mglmOneWay() (in module inmoose.edgepy) movingAverageByCol() (in module inmoose.edgepy)

N

nbinomDeviance() (in module inmoose.edgepy) nbinomLRT() (in module inmoose.deseq2)

nbinomWaldTest() (in module inmoose.deseq2) normalizationFactors (inmoose.deseq2.DESeqDataSet.DESeqDataSet property)

O

offset (inmoose.edgepy.DGEList attribute)

P

p_adjust() (in module inmoose.deseq2.results) pasilla() (in module inmoose.data.pasilla) predFC() (in module inmoose.edgepy)

priorInfo (inmoose.deseq2.results.DESeqResults attribute) pycombat_norm() (in module inmoose.pycombat) pycombat_seq() (in module inmoose.pycombat)

R

replaceOutliers() (in module inmoose.deseq2)

results() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) rnbinom() (in module inmoose.utils)

S

samples (inmoose.edgepy.DGEList attribute) setDispFunction() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) sim_rnaseq() (in module inmoose.sim)

sizeFactors (inmoose.deseq2.DESeqDataSet.DESeqDataSet property) splitIntoGroups() (in module inmoose.edgepy) systematicSubset() (in module inmoose.edgepy)

T

tagwise_dispersion (inmoose.edgepy.DGEList attribute)

trended_dispersion (inmoose.edgepy.DGEList attribute)

V

validDGEList() (in module inmoose.edgepy)

varianceStabilizingTransformation() (in module inmoose.deseq2)

W

wtd_quantile() (in module inmoose.deseq2.Hmisc)