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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 |
| Author: | Ahmed Alhendi [aut, cre] |
| Maintainer: | Ahmed Alhendi <asna4 at le.ac.uk> |
| BugReports: | https://github.com/AAlhendi1707/countToFPKM/issues |
| License: | GPL-3 |
| URL: | https://github.com/AAlhendi1707/countToFPKM |
| NeedsCompilation: | no |
| CRAN checks: | countToFPKM results |
| Reference manual: | countToFPKM.pdf |
| Package source: | countToFPKM_1.0.tar.gz |
| Windows binaries: | r-devel: countToFPKM_1.0.zip, r-release: countToFPKM_1.0.zip, r-oldrel: countToFPKM_1.0.zip |
| 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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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.