metaseqR2
metaseqR2 is a Bioconductor package for the analysis of RNA-Seq data with multiple algorithms based on the PANDORA p-value combination method. PANDORA combines multiple statistical tests through the systematic combination of individual tests by weighting their outcomes according to their performance with realistically simulated data sets generated from real data.
Apart from PANDORA, metaseqR2 offers an interface to:
- 9 statistical tests for RNA-Seq data (DESeq, DESeq2, edgeR, voom, NBPSeq, baySeq, NOISeq, ABSSeq, DSS)
- 8 normalization methods (DESeq, DESeq2, EDASeq, edgeR, NBPSeq, NOISeq, ABSSeq, DSS)
- 7 p-value combination methods (PANDORA, Simes, Fisher, Union, Intersection, Whitlock, Harmonic mean)
- An automatic annotation retrieval and build system
- A complete end-to-end pipeline for the analysis of RNA-Seq data, starting from BAM files up to reporting of the results
- A wealth of exported data summary values and metrics at various scales
- Industrial-level, fully interactive report of the results with numerous quality control and result exploration interactive graphs and tables.
- Special modules for the analysis of 3’ UTR sequencing protocols.
Availability: