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
countToFPKM_1.2.0.zip(r-4.7)countToFPKM_1.2.0.zip(r-4.6)countToFPKM_1.2.0.zip(r-4.5)
countToFPKM_1.2.0.tgz(r-4.6-any)countToFPKM_1.2.0.tgz(r-4.5-any)
countToFPKM_1.2.0.tar.gz(r-4.7-any)countToFPKM_1.2.0.tar.gz(r-4.6-any)
countToFPKM_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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 from:674bbeb3d0. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 166 | ||
| source / vignettes | OK | 157 | ||
| linux-release-x86_64 | NOTE | 147 | ||
| macos-release-arm64 | NOTE | 167 | ||
| macos-oldrel-arm64 | NOTE | 231 | ||
| windows-devel | NOTE | 99 | ||
| windows-release | NOTE | 102 | ||
| windows-oldrel | NOTE | 89 | ||
| wasm-release | OK | 107 |
Exports:fpkmfpkmheatmap
Dependencies:BiocGenericscirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayondigestdoParallelforeachgenericsGetoptLongGlobalOptionsIRangesiteratorsmatrixStatspngRColorBrewerrjsonS4Vectorsshape
