Introduction | Data set quality control in anota | Using anota to identify differential translation | Random variance model (RVM) to improve power in detection of differential translational activity within anota | Data set requirements for application of anota | Example
Package: anota 1.61.0
Ola Larsson
anota: ANalysis Of Translational Activity (ANOTA).
Genome wide studies of translational control is emerging as a tool to study verious biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis.
Authors:
anota_1.61.0.tar.gz
anota_1.61.0.zip(r-4.7)anota_1.61.0.zip(r-4.6)anota_1.61.0.zip(r-4.5)
anota_1.61.0.tgz(r-4.6-any)anota_1.61.0.tgz(r-4.5-any)
anota_1.61.0.tar.gz(r-4.7-any)anota_1.61.0.tar.gz(r-4.6-any)
anota_1.61.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
anota/json (API)
| # Install 'anota' in R: |
| install.packages('anota', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- anotaDataP - Sample data set for anota
- anotaDataT - Sample data set for anota
- anotaPhenoVec - Sample data set for anota
On BioConductor:anota-1.61.0(bioc 3.24)anota-1.60.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressiondifferentialexpressionmicroarraysequencing
Last updated from:e906dc11d3. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 149 | ||
| linux-devel-x86_64 | NOTE | 186 | ||
| source / vignettes | OK | 208 | ||
| linux-release-x86_64 | NOTE | 211 | ||
| macos-release-arm64 | NOTE | 151 | ||
| macos-oldrel-arm64 | NOTE | 81 | ||
| windows-devel | NOTE | 109 | ||
| windows-release | NOTE | 104 | ||
| windows-oldrel | NOTE | 105 | ||
| wasm-release | OK | 146 |
Exports:anotaGetSigGenesanotaPerformQcanotaPlotSigGenesanotaResidOutlierTest
Dependencies:BiobaseBiocGenericsclicpp11farvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmulttestplyrqvalueR6RColorBrewerRcppreshape2rlangS7scalesstringistringrsurvivalvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Sample data set for anota | anotaDataP anotaDataSet anotaDataT anotaPhenoVec |
| Identify genes that are under translational control independent of cytosolic mRNA levels | anotaGetSigGenes |
| Perform quality control to ensure that the supplied data set is suitable for Analysis of Partial Variance (APV) within anota. | anotaPerformQc |
| Filter and plot genes to visualize/summarize genes that are differentially translated. | anotaPlotSigGenes |
| Test for normality of residuals | anotaResidOutlierTest |
