buildAnnotationDatabase
                        Build a local annotation database for metaseqR2
buildCustomAnnotation   Import custom annotation to the metaseqR2
                        annotation database from GTF file
combineBonferroni       Combine p-values with Bonferroni's method
combineHarmonic         Combine p-values using weights
combineMaxp             Combine p-values using the maximum p-value
combineMinp             Combine p-values using the minimum p-value
combineSimes            Combine p-values with Simes' method
combineWeight           Combine p-values using weights
createSignalTracks      Create bigWig signal tracks
diagplotAvgFtd          Create average False (or True) Discovery curves
diagplotBoxplot         Boxplots wrapper for the metaseqR2 package
diagplotCor             Summarized correlation plots
diagplotDeHeatmap       Diagnostic heatmap of differentially expressed
                        genes
diagplotEdaseq          Diagnostic plots based on the EDASeq package
diagplotFiltered        Diagnostic plot for filtered genes
diagplotFtd             Create False (or True) Positive (or Negative)
                        curves
diagplotMds             Multi-Dimensinal Scale plots or RNA-Seq samples
diagplotNoiseq          Diagnostic plots based on the NOISeq package
diagplotPairs           Massive X-Y, M-D correlation plots
diagplotRoc             Create basic ROC curves
diagplotVenn            Venn diagrams when performing meta-analysis
diagplotVolcano         (Interactive) volcano plots of differentially
                        expressed genes
downsampleCounts        Downsample read counts
estimateAufcWeights     Estimate AUFC weights
estimateSimParams       Estimate negative binomial parameters from real
                        data
getAnnotation           Annotation downloader
getDefaults             Default parameters for several metaseqr
                        functions
getInstalledAnnotations
                        Load a metaseqR2 annotation element
getWeights              Get precalculated statistical test weights
hg19pvalues             p-values from human RNA-Seq data with two
                        conditions, four samples
importCustomAnnotation
                        Import a metaseqR2 custom annotation element
libsizeListMm9          Mouse RNA-Seq data with two conditions, four
                        samples
loadAnnotation          Load a metaseqR2 annotation element
makeSimDataSd           Create simulated counts using the
                        Soneson-Delorenzi method
makeSimDataTcc          Create simulated counts using TCC package
metaseqr2               The main metaseqr2 pipeline
metaseqrPlot            Diagnostic plots for the metaseqR2 package
metaTest                Meta-analysis using several RNA-Seq statistics
mm9GeneCounts           Mouse RNA-Seq data with two conditions, four
                        samples
normalizeAbsseq         Normalization based on the ABSSeq package
normalizeDeseq          Normalization based on the DESeq package
normalizeDeseq2         Normalization based on the DESeq2 package
normalizeDss            Normalization based on the DSS package
normalizeEdaseq         Normalization based on the EDASeq package
normalizeEdger          Normalization based on the edgeR package
normalizeNbpseq         Normalization based on the NBPSeq package
normalizeNoiseq         Normalization based on the NOISeq package
read2count              SAM/BAM/BED file reader helper for the
                        metaseqr2 pipeline
readTargets             Creates sample list and BAM/BED file list from
                        file
sampleListMm9           Mouse RNA-Seq data with two conditions, four
                        samples
statAbsseq              Statistical testing with ABSSeq
statDeseq               Statistical testing with DESeq
statDeseq2              Statistical testing with DESeq2
statDss                 Statistical testing with DSS
statEdger               Statistical testing with edgeR
statLimma               Statistical testing with limma
statNbpseq              Statistical testing with NBPSeq
statNoiseq              Statistical testing with NOISeq
