Man pages for pmoulos/metaseqR2
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
| buildAnnotationDatabase | Build a local annotation database for metaseqR2 |
| buildCustomAnnotation | Import custom annotation to the metaseqR2 annotation database... |
| 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... |
| 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 |
