Index

_

__init__() (inmoose.consensus_clustering.consensus_clustering.consensusClustering method) (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) (inmoose.diffexp.DEResults.DEResults method) (inmoose.edgepy.DGEList method) (inmoose.limma.MArrayLM method) (inmoose.limma.TestResults method) (inmoose.utils.Factor method) (inmoose.utils.lm_fit method) (inmoose.utils.lm_wfit method)

A

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

Amean (inmoose.limma.MArrayLM attribute) AveLogCPM (inmoose.edgepy.DGEList attribute) aveLogCPM() (in module inmoose.edgepy)

B

binomTest() (in module inmoose.edgepy)

C

classifyTestsF() (in module inmoose.limma) coefficients (inmoose.limma.MArrayLM attribute) collapseReplicates() (in module inmoose.deseq2) common_dispersion (inmoose.edgepy.DGEList attribute) consensusClustering (class in inmoose.consensus_clustering.consensus_clustering)

contrasts (inmoose.limma.MArrayLM attribute) contrasts_fit() (in module inmoose.limma) counts (inmoose.edgepy.DGEList attribute) counts() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) cov_coefficients (inmoose.limma.MArrayLM attribute)

D

DEResults (class in inmoose.diffexp.DEResults) DESeq() (in module inmoose.deseq2) DESeqDataSet (class in inmoose.deseq2.DESeqDataSet) DESeqResults (class in inmoose.deseq2.results) design (inmoose.deseq2.DESeqDataSet.DESeqDataSet property) (inmoose.limma.MArrayLM attribute) designAsFactor() (in module inmoose.edgepy)

df_prior (inmoose.limma.MArrayLM attribute) df_residual (inmoose.limma.MArrayLM attribute) df_total (inmoose.limma.MArrayLM attribute) 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

eBayes() (in module inmoose.limma) 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) exactTest() (in module inmoose.edgepy) exactTestBetaApprox() (in module inmoose.edgepy) exactTestByDeviance() (in module inmoose.edgepy) exactTestBySmallP() (in module inmoose.edgepy) exactTestDoubleTail() (in module inmoose.edgepy)

F

F (inmoose.limma.MArrayLM attribute) F_p_value (inmoose.limma.MArrayLM attribute)

Factor (class in inmoose.utils) filtered_p() (in module inmoose.deseq2.results) fitFDist() (in module inmoose.limma)

G

genes (inmoose.edgepy.DGEList attribute) (inmoose.limma.MArrayLM attribute) glmFit() (in module inmoose.edgepy)

glmLRT() (in module inmoose.edgepy) glmQLFit() (in module inmoose.edgepy) glmQLFTest() (in module inmoose.edgepy)

L

lm_fit (class in inmoose.utils) lm_series() (in module inmoose.limma)

lm_wfit (class in inmoose.utils) lmFit() (in module inmoose.limma) lods (inmoose.limma.MArrayLM attribute)

M

makeContrasts() (in module inmoose.limma) makeExampleDESeqDataSet() (in module inmoose.deseq2) MArrayLM (class in inmoose.limma) meta_de() (in module inmoose.diffexp)

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) p_value (inmoose.limma.MArrayLM attribute) pasilla() (in module inmoose.data.pasilla) plotMA() (inmoose.diffexp.DEResults.DEResults method)

plotQLDisp() (in module inmoose.edgepy) 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

s2_post (inmoose.limma.MArrayLM attribute) s2_prior (inmoose.limma.MArrayLM attribute) samples (inmoose.edgepy.DGEList attribute) setDispFunction() (inmoose.deseq2.DESeqDataSet.DESeqDataSet method) sigma (inmoose.limma.MArrayLM attribute)

sim_rnaseq() (in module inmoose.sim) sizeFactors (inmoose.deseq2.DESeqDataSet.DESeqDataSet property) splitIntoGroups() (in module inmoose.edgepy) squeezeVar() (in module inmoose.limma) stdev_unscaled (inmoose.limma.MArrayLM attribute) systematicSubset() (in module inmoose.edgepy)

T

t (inmoose.limma.MArrayLM attribute) tagwise_dispersion (inmoose.edgepy.DGEList attribute) TestResults (class in inmoose.limma) tmixture_matrix() (in module inmoose.limma)

tmixture_vector() (in module inmoose.limma) topTable() (in module inmoose.limma) topTags() (in module inmoose.edgepy) trended_dispersion (inmoose.edgepy.DGEList attribute)

V

validDGEList() (in module inmoose.edgepy)

var_prior (inmoose.limma.MArrayLM attribute) varianceStabilizingTransformation() (in module inmoose.deseq2)

W

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