AAlhendi1707/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.

Getting started

Package details

AuthorAhmed Alhendi (Dr.)
MaintainerAhmed Alhendi <[email protected]>
URL https://github.com/AAlhendi1707/countToFPKM
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
AAlhendi1707/countToFPKM documentation built on Aug. 10, 2019, 3:39 p.m.