Package: anota2seq 1.35.0

Christian Oertlin

anota2seq: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

anota2seq provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source (i.e. translated mRNA or total mRNA). Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels (i.e. changes in translated mRNA that are independent of levels of total mRNA) or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels (i.e. changes in total mRNA that are independent of levels of translated mRNA). anota2seq applies analysis of partial variance and the random variance model to fulfill these tasks.

Authors:Christian Oertlin <[email protected]>, Julie Lorent <[email protected]>, Ola Larsson <[email protected]>

anota2seq_1.35.0.tar.gz
anota2seq_1.35.0.zip(r-4.7)anota2seq_1.35.0.zip(r-4.6)anota2seq_1.35.0.zip(r-4.5)
anota2seq_1.35.0.tgz(r-4.6-any)anota2seq_1.35.0.tgz(r-4.5-any)
anota2seq_1.35.0.tar.gz(r-4.7-any)anota2seq_1.35.0.tar.gz(r-4.6-any)
anota2seq_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
anota2seq/json (API)

# Install 'anota2seq' in R:

install.packages('anota2seq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

anota2seq_data_P - Sample data set for anota2seq
anota2seq_data_T - Sample data set for anota2seq
anota2seq_pheno_vec - Sample data set for anota2seq

On BioConductor:anota2seq-1.35.0(bioc 3.24)anota2seq-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology geneexpression differentialexpression microarray genomewideassociation batcheffect normalization rnaseq sequencing generegulation regression

5.04 score 1 packages 23 scripts 8 mentions 19 exports 58 dependencies

Last updated from:45159c579c. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	194
linux-devel-x86_64	OK	383
source / vignettes	OK	393
linux-release-x86_64	OK	337
macos-release-arm64	OK	178
macos-oldrel-arm64	OK	203
windows-devel	OK	291
windows-release	OK	305
windows-oldrel	OK	265
wasm-release	OK	171

Exports:anota2seqAnalyze anota2seqDataSetFromMatrix anota2seqDataSetFromSE anota2seqGetContrasts anota2seqGetCovariates anota2seqGetDeltaData anota2seqGetNormalizedData anota2seqGetOutput anota2seqGetQualityControl anota2seqGetResidOutlierTest anota2seqGetThresholds anota2seqPerformQC anota2seqPlotFC anota2seqPlotGenes anota2seqPlotPvalues anota2seqRegModes anota2seqResidOutlierTest anota2seqRun anota2seqSelSigGenes

Dependencies:abind BH Biobase BiocGenerics BiocParallel cli codetools cpp11 DelayedArray DESeq2 edgeR farver formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats multtest plyr qvalue R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment survival vctrs viridisLite withr XVector

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Rendered fromanota2seq.Rnwusingknitr::knitr

Last update: 2019-01-24
Started: 2017-09-04

Help page	Topics
Sample data set for anota2seq	anota2seq_data anota2seq_data_P anota2seq_data_T anota2seq_pheno_vec
Visualization of anota2seq results	anota2seq-plots anota2seqPlotFC anota2seqPlotFC,Anota2seqDataSet-method anota2seqPlotGenes anota2seqPlotGenes,Anota2seqDataSet-method anota2seqPlotPvalues anota2seqPlotPvalues,Anota2seqDataSet-method
Analysis of translational activity	anota2seqAnalyze
Anota2seqDataSet class	Anota2seqDataSet Anota2seqDataSet-class
Anota2seqDataSet constructors.	anota2seqDataSetFromMatrix anota2seqDataSetFromSE
Accessor for the 'contrasts' slot of an Anota2seqDataSet object.	anota2seqGetContrasts anota2seqGetContrasts,Anota2seqDataSet-method
Accessor for the 'phenoVec' and 'batchVec' slots of an Anota2seqDataSet object.	anota2seqGetCovariates anota2seqGetCovariates,Anota2seqDataSet-method
Accessor for the fold changes and TE scores stored in the 'deltaData' slot of an Anota2seqDataSet object.	anota2seqGetDeltaData anota2seqGetDeltaData,Anota2seqDataSet-method
Accessor for the 'normalizedDataP' and 'normalizedDataT' slots of an Anota2seqDataSet object.	anota2seqGetNormalizedData anota2seqGetNormalizedData,Anota2seqDataSet-method
Retrieve output for analyzes stored in the Anota2seqDataSet	anota2seqGetOutput anota2seqGetOutput,Anota2seqDataSet-method
Retrieve the anota2seqPerformQC output from the Anota2seqDataSet	anota2seqGetQualityControl anota2seqGetQualityControl,Anota2seqDataSet-method
Retrieve residOutlierTest	anota2seqGetResidOutlierTest anota2seqGetResidOutlierTest,Anota2seqDataSet-method
Get filtering criteria thresholds	anota2seqGetThresholds anota2seqGetThresholds,Anota2seqDataSet-method
Perform quality control to ensure that the supplied data set is suitable for Analysis of Partial Variance (APV) within anota2seq.	anota2seqPerformQC
Categorize genes into regulatory modes of gene expression (mRNA abundance or changes in translational efficiency leading to altered protein levels or buffering)	anota2seqRegModes
Test for normality of residuals	anota2seqResidOutlierTest
Wrapper for several functions which provide one-step analysis	anota2seqRun
Select identifiers from the output of 'anota2seqAnalyze'.	anota2seqSelSigGenes
Show information for an Anota2seqDataSet	show show,Anota2seqDataSet-method

Package: anota2seq 1.35.0

anota2seq: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)