countToFPKM: Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

Implements the algorithm described in Trapnell,C. et al. (2010) <doi:10.1038/nbt.1621>. This function takes read counts matrix of RNA-Seq data, feature lengths which can be retrieved using 'biomaRt' package, and the mean fragment lengths which can be calculated using the 'CollectInsertSizeMetrics(Picard)' tool. It then returns a matrix of FPKM normalised data by library size and feature effective length. It also provides the user with a quick and reliable function to generate FPKM heatmap plot of the highly variable features in RNA-Seq dataset.

Version: 1.0
Depends: R (≥ 3.1.0), ComplexHeatmap, circlize, stats
Published: 2019-04-07
DOI: 10.32614/CRAN.package.countToFPKM
Author: Ahmed Alhendi [aut, cre]
Maintainer: Ahmed Alhendi <asna4 at>
License: GPL-3
NeedsCompilation: no
CRAN checks: countToFPKM results


Reference manual: countToFPKM.pdf


Package source: countToFPKM_1.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): countToFPKM_1.0.tgz, r-oldrel (arm64): countToFPKM_1.0.tgz, r-release (x86_64): countToFPKM_1.0.tgz, r-oldrel (x86_64): countToFPKM_1.0.tgz


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