DegNorm-package: DegNorm: degradation normalization for RNA-seq data

In jipingw/DegNorm: DegNorm: degradation normalization for RNA-seq data

DegNorm: degradation normalization for RNA-seq data

Description

DegNorm is an R package for degradation normalication for bulk RNA-seq data.DegNorm, short for degradation normalization, is a bioinformatics pipeline designed to correct for bias due to the heterogeneous patterns of transcript degradation in RNA-seq data.

Details

DegNorm is a data-driven approach for RNA-Seq normalization resulting in the adjusted read count matrix. This adjustment applies to each gene within each sample, accounting for sample- and gene-specific degradation bias while simultaneously controlling for the sequencing depth. The algorithm at the center of DegNorm is the rank-one over-approximation of a gene's coverage score matrix, which is comprised of the different samples' coverage score curves along the transcript for each gene. For each gene, DegNorm estimates (1) an envelope function representing the ideal shape of the gene's coverage curve when no degradation is present, and (2) scale factors for each sample (for said gene) that indicates the relative abundance of the gene within the sample.

functions: read_coverage_batch, degnorm, plot_coverage, plot_heatmap, plot_corr, plot_boxplot

Author(s)

Bin Xiong, Ji-Ping Wang

Maintainer: Ji-Ping Wang <[e-mail]>

References

DegNorm reference:

Xiong, B., Yang, Y., Fineis, F. Wang, J.-P., DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis, Genome Biology, 2019,20:75

jipingw/DegNorm documentation built on April 3, 2024, 1:22 a.m.