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countToFPKM
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Download and install countToFPKM package within the R console
Install from CRAN:
install.packages("countToFPKM")
Install from Github:
library("remotes")
install_github("cran/countToFPKM")
Install by package version:
library("remotes")
install_version("countToFPKM", "1.0")
Attach the package and use:
library("countToFPKM")
Maintained by
Ahmed Alhendi
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All associated links for this package
First Published: 2019-04-07
Latest Update: 2019-04-07
Description:
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.
How to cite:
Ahmed Alhendi (2019). countToFPKM: Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM). R package version 1.0, https://cran.r-project.org/web/packages/countToFPKM. Accessed 21 Nov. 2024.
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Complete documentation for countToFPKM
Functions, R codes and Examples using
the countToFPKM R package
Some associated functions: fpkm . fpkmheatmap .
Some associated R codes: countToFPKM-internal.R . Full countToFPKM package functions and examples
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