Package: countToFPKM 1.2.0

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.

Authors:Ahmed Alhendi

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Bug tracker:https://github.com/aalhendi1707/counttofpkm/issues

On CRAN:

gene-expressionnormalizationrna-seq

2 exports 61 stars 3.48 score 21 dependencies 2 mentions 20 scripts 232 downloads

Last updated 3 years agofrom:674bbeb3d0. Checks:OK: 1 NOTE: 6. Indexed: yes.

Exports:fpkmfpkmheatmap

Dependencies:BiocGenericscirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayondigestdoParallelforeachGetoptLongGlobalOptionsIRangesiteratorsmatrixStatspngRColorBrewerrjsonS4Vectorsshape