Package: anota2seq 1.29.0

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]>

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anota2seq.pdf |anota2seq.html✨
anota2seq/json (API)
NEWS

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

Peer review:

Datasets:

On BioConductor:anota2seq-1.29.0(bioc 3.21)anota2seq-1.28.0(bioc 3.20)

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

immunooncologygeneexpressiondifferentialexpressionmicroarraygenomewideassociationbatcheffectnormalizationrnaseqsequencinggeneregulationregression

4.28 score 12 scripts 402 downloads 8 mentions 19 exports 77 dependencies

Last updated 2 months agofrom:9a745aaeac. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:anota2seqAnalyzeanota2seqDataSetFromMatrixanota2seqDataSetFromSEanota2seqGetContrastsanota2seqGetCovariatesanota2seqGetDeltaDataanota2seqGetNormalizedDataanota2seqGetOutputanota2seqGetQualityControlanota2seqGetResidOutlierTestanota2seqGetThresholdsanota2seqPerformQCanota2seqPlotFCanota2seqPlotGenesanota2seqPlotPvaluesanota2seqRegModesanota2seqResidOutlierTestanota2seqRunanota2seqSelSigGenes

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurlDelayedArrayDESeq2edgeRfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemulttestmunsellnlmeopensslpillarpkgconfigplyrqvalueR6RColorBrewerRcppRcppArmadilloreshape2rlangS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Rendered fromanota2seq.Rnwusingknitr::knitron Nov 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Sample data set for anota2seqanota2seq_data anota2seq_data_P anota2seq_data_T anota2seq_pheno_vec
Visualization of anota2seq resultsanota2seq-plots anota2seqPlotFC anota2seqPlotFC,Anota2seqDataSet-method anota2seqPlotGenes anota2seqPlotGenes,Anota2seqDataSet-method anota2seqPlotPvalues anota2seqPlotPvalues,Anota2seqDataSet-method
Analysis of translational activityanota2seqAnalyze
Anota2seqDataSet classAnota2seqDataSet 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 Anota2seqDataSetanota2seqGetOutput anota2seqGetOutput,Anota2seqDataSet-method
Retrieve the anota2seqPerformQC output from the Anota2seqDataSetanota2seqGetQualityControl anota2seqGetQualityControl,Anota2seqDataSet-method
Retrieve residOutlierTestanota2seqGetResidOutlierTest anota2seqGetResidOutlierTest,Anota2seqDataSet-method
Get filtering criteria thresholdsanota2seqGetThresholds 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 residualsanota2seqResidOutlierTest
Wrapper for several functions which provide one-step analysisanota2seqRun
Select identifiers from the output of 'anota2seqAnalyze'.anota2seqSelSigGenes
Show information for an Anota2seqDataSetshow show,Anota2seqDataSet-method