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:
countToFPKM_1.2.0.tar.gz
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countToFPKM_1.2.0.tar.gz(r-4.5-noble)countToFPKM_1.2.0.tar.gz(r-4.4-noble)
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countToFPKM.pdf |countToFPKM.html✨
countToFPKM/json (API)
| # Install 'countToFPKM' in R: |
| install.packages('countToFPKM', repos = c('https://aalhendi1707.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/aalhendi1707/counttofpkm/issues
gene-expressionnormalizationrna-seq
Last updated 4 years agofrom:674bbeb3d0. Checks:1 OK, 8 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 25 2025 |
| R-4.5-win | NOTE | Mar 25 2025 |
| R-4.5-mac | NOTE | Mar 25 2025 |
| R-4.5-linux | NOTE | Mar 25 2025 |
| R-4.4-win | NOTE | Mar 25 2025 |
| R-4.4-mac | NOTE | Mar 25 2025 |
| R-4.4-linux | NOTE | Mar 25 2025 |
| R-4.3-win | NOTE | Mar 25 2025 |
| R-4.3-mac | NOTE | Mar 25 2025 |
Exports:fpkmfpkmheatmap
Dependencies:BiocGenericscirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayondigestdoParallelforeachgenericsGetoptLongGlobalOptionsIRangesiteratorsmatrixStatspngRColorBrewerrjsonS4Vectorsshape
