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

Implements the algorithm described in Trapnell,C. et al. (2010) . 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.


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install.packages("countToFPKM")

1.0 by Ahmed Alhendi, 3 months ago


https://github.com/AAlhendi1707/countToFPKM


Report a bug at https://github.com/AAlhendi1707/countToFPKM/issues


Browse source code at https://github.com/cran/countToFPKM


Authors: Ahmed Alhendi [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Depends on ComplexHeatmap, circlize, stats


See at CRAN