aggregateBySample | Aggregates a MRexperiment object or counts matrix to by a... |
aggregateByTaxonomy | Aggregates a MRexperiment object or counts matrix to a... |
biom2MRexperiment | Biom to MRexperiment objects |
calcNormFactors | Cumulative sum scaling (css) normalization factors |
calcPosComponent | Positive component |
calcShrinkParameters | Calculate shrinkage parameters |
calcStandardError | Calculate the zero-inflated log-normal statistic's standard... |
calculateEffectiveSamples | Estimated effective samples per feature |
calcZeroAdjustment | Calculate the zero-inflated component's adjustment factor |
calcZeroComponent | Zero component |
correctIndices | Calculate the correct indices for the output of... |
correlationTest | Correlation of each row of a matrix or MRexperiment object |
cumNorm | Cumulative sum scaling normalization |
cumNormMat | Cumulative sum scaling factors. |
cumNormStat | Cumulative sum scaling percentile selection |
cumNormStatFast | Cumulative sum scaling percentile selection |
doCountMStep | Compute the Maximization step calculation for features still... |
doEStep | Compute the Expectation step. |
doZeroMStep | Compute the zero Maximization step. |
exportMat | Export the normalized MRexperiment dataset as a matrix. |
exportStats | Various statistics of the count data. |
expSummary | Access MRexperiment object experiment data |
extractMR | Extract the essentials of an MRexperiment. |
filterData | Filter datasets according to no. features present in features... |
fitDO | Wrapper to calculate Discovery Odds Ratios on feature values. |
fitFeatureModel | Computes differential abundance analysis using a... |
fitFeatureModelResults-class | Class "fitFeatureModelResults" - a formal class for storing... |
fitLogNormal | Computes a log-normal linear model and permutation based... |
fitMultipleTimeSeries | Discover differentially abundant time intervals for all... |
fitPA | Wrapper to run fisher's test on presence/absence of a... |
fitSSTimeSeries | Discover differentially abundant time intervals using... |
fitTimeSeries | Discover differentially abundant time intervals |
fitZeroLogNormal | Compute the log fold-change estimates for the zero-inflated... |
fitZig | Computes the weighted fold-change estimates and t-statistics. |
fitZigResults-class | Class "fitZigResults" - a formal class for storing results... |
getCountDensity | Compute the value of the count density function from the... |
getEpsilon | Calculate the relative difference between iterations of the... |
getNegativeLogLikelihoods | Calculate the negative log-likelihoods for the various... |
getPi | Calculate the mixture proportions from the zero model / spike... |
getZ | Calculate the current Z estimate responsibilities (posterior... |
isItStillActive | Function to determine if a feature is still active. |
libSize | Access sample depth of coverage from MRexperiment object |
libSize-set | Replace the library sizes in a MRexperiment object |
loadBiom | Load objects organized in the Biom format. |
loadMeta | Load a count dataset associated with a study. |
loadMetaQ | Load a count dataset associated with a study set up in a... |
loadPhenoData | Load a clinical/phenotypic dataset associated with a study. |
lungData | OTU abundance matrix of samples from a smoker/non-smoker... |
makeLabels | Function to make labels simpler |
mergeMRexperiments | Merge two MRexperiment objects together |
mergeTable | Merge two tables |
metagenomeSeq-deprecated | Depcrecated functions in the metagenomeSeq package. |
metagenomeSeq-package | Statistical analysis for sparse high-throughput sequencing |
mouseData | OTU abundance matrix of mice samples from a diet longitudinal... |
MRcoefs | Table of top-ranked features from fitZig or fitFeatureModel |
MRcounts | Accessor for the counts slot of a MRexperiment object |
MRexperiment2biom | MRexperiment to biom objects |
MRexperiment-class | Class "MRexperiment" - a modified eSet object for the data... |
MRfulltable | Table of top microbial marker gene from linear model fit... |
MRihw | MRihw runs IHW within a MRcoefs() call |
MRihw-fitFeatureModelResults | MRihw runs IHW within a MRcoefs() call |
MRihw-fitZigResults | MRihw runs IHW within a MRcoefs() call |
MRtable | Table of top microbial marker gene from linear model fit... |
newMRexperiment | Create a MRexperiment object |
normFactors | Access the normalization factors in a MRexperiment object |
normFactors-set | Replace the normalization factors in a MRexperiment object |
plotBubble | Basic plot of binned vectors. |
plotClassTimeSeries | Plot abundances by class |
plotCorr | Basic correlation plot function for normalized or... |
plotFeature | Basic plot function of the raw or normalized data. |
plotGenus | Basic plot function of the raw or normalized data. |
plotMRheatmap | Basic heatmap plot function for normalized counts. |
plotOrd | Plot of either PCA or MDS coordinates for the distances of... |
plotOTU | Basic plot function of the raw or normalized data. |
plotRare | Plot of rarefaction effect |
plotTimeSeries | Plot difference function for particular bacteria |
posteriorProbs | Access the posterior probabilities that results from analysis |
returnAppropriateObj | Check if MRexperiment or matrix and return matrix |
ssFit | smoothing-splines anova fit |
ssIntervalCandidate | calculate interesting time intervals |
ssPerm | class permutations for smoothing-spline time series analysis |
ssPermAnalysis | smoothing-splines anova fits for each permutation |
trapz | Trapezoidal Integration |
ts2MRexperiment | With a list of fitTimeSeries results, generate an... |
uniqueFeatures | Table of features unique to a group |
wrenchNorm | Computes normalization factors using wrench instead of... |
zigControl | Settings for the fitZig function |
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