Man pages for metaseqR2
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

buildAnnotationDatabaseBuild a local annotation database for metaseqR2
buildCustomAnnotationImport custom annotation to the metaseqR2 annotation database...
combineBonferroniCombine p-values with Bonferroni's method
combineHarmonicCombine p-values using weights
combineMaxpCombine p-values using the maximum p-value
combineMinpCombine p-values using the minimum p-value
combineSimesCombine p-values with Simes' method
combineWeightCombine p-values using weights
createSignalTracksCreate bigWig signal tracks
diagplotAvgFtdCreate average False (or True) Discovery curves
diagplotBoxplotBoxplots wrapper for the metaseqR2 package
diagplotCorSummarized correlation plots
diagplotDeHeatmapDiagnostic heatmap of differentially expressed genes
diagplotEdaseqDiagnostic plots based on the EDASeq package
diagplotFilteredDiagnostic plot for filtered genes
diagplotFtdCreate False (or True) Positive (or Negative) curves
diagplotMdsMulti-Dimensinal Scale plots or RNA-Seq samples
diagplotNoiseqDiagnostic plots based on the NOISeq package
diagplotPairsMassive X-Y, M-D correlation plots
diagplotRocCreate basic ROC curves
diagplotVennVenn diagrams when performing meta-analysis
diagplotVolcano(Interactive) volcano plots of differentially expressed genes
downsampleCountsDownsample read counts
estimateAufcWeightsEstimate AUFC weights
estimateSimParamsEstimate negative binomial parameters from real data
getAnnotationAnnotation downloader
getDefaultsDefault parameters for several metaseqr functions
getInstalledAnnotationsLoad a metaseqR2 annotation element
getWeightsGet precalculated statistical test weights
hg19pvaluesp-values from human RNA-Seq data with two conditions, four...
importCustomAnnotationImport a metaseqR2 custom annotation element
libsizeListMm9Mouse RNA-Seq data with two conditions, four samples
loadAnnotationLoad a metaseqR2 annotation element
makeSimDataSdCreate simulated counts using the Soneson-Delorenzi method
makeSimDataTccCreate simulated counts using TCC package
metaseqr2The main metaseqr2 pipeline
metaseqrPlotDiagnostic plots for the metaseqR2 package
metaTestMeta-analysis using several RNA-Seq statistics
mm9GeneCountsMouse RNA-Seq data with two conditions, four samples
normalizeAbsseqNormalization based on the ABSSeq package
normalizeDeseqNormalization based on the DESeq package
normalizeDeseq2Normalization based on the DESeq2 package
normalizeDssNormalization based on the DSS package
normalizeEdaseqNormalization based on the EDASeq package
normalizeEdgerNormalization based on the edgeR package
normalizeNbpseqNormalization based on the NBPSeq package
normalizeNoiseqNormalization based on the NOISeq package
read2countSAM/BAM/BED file reader helper for the metaseqr2 pipeline
readTargetsCreates sample list and BAM/BED file list from file
sampleListMm9Mouse RNA-Seq data with two conditions, four samples
statAbsseqStatistical testing with ABSSeq
statBayseqStatistical testing with baySeq
statDeseqStatistical testing with DESeq
statDeseq2Statistical testing with DESeq2
statDssStatistical testing with DSS
statEdgerStatistical testing with edgeR
statLimmaStatistical testing with limma
statNbpseqStatistical testing with NBPSeq
statNoiseqStatistical testing with NOISeq
metaseqR2 documentation built on Nov. 8, 2020, 7:34 p.m.