An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

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Documentation for package ‘metaseqR2’ version 1.21.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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