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 |

statBayseq | Statistical testing with baySeq |

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 |

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