Package: compcodeR 1.43.0

Charlotte Soneson

compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

Authors:Charlotte Soneson [aut, cre], Paul Bastide [aut], Mélina Gallopin [aut]

compcodeR_1.43.0.tar.gz
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compcodeR.pdf |compcodeR.html✨
compcodeR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/csoneson/compcoder/issues

On BioConductor:compcodeR-1.43.0(bioc 3.21)compcodeR-1.42.0(bioc 3.20)

immunooncologyrnaseqdifferentialexpression

7.92 score 10 stars 26 scripts 252 downloads 11 mentions 36 exports 97 dependencies

Last updated 19 days agofrom:fdc74f1b59. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winNOTENov 03 2024
R-4.5-linuxNOTENov 03 2024
R-4.4-winNOTENov 03 2024
R-4.4-macNOTENov 03 2024
R-4.3-winOKNov 03 2024
R-4.3-macOKNov 03 2024

Exports:check_compDatacheck_compData_resultscheck_phyloCompDatacheckDataObjectcheckTableConsistencycompDataconvertcompDataToListconvertListTocompDataconvertListTophyloCompDataconvertphyloCompDataToListDESeq2.createRmdDESeq2.length.createRmdDSS.createRmdEBSeq.createRmdedgeR.exact.createRmdedgeR.GLM.createRmdgenerateCodeHTMLsgenerateSyntheticDatalengthNorm.limma.createRmdlengthNorm.sva.limma.createRmdlistcreateRmdlogcpm.limma.createRmdNBPSeq.createRmdNOISeq.prenorm.createRmdphyloCompDataphylolm.createRmdrunComparisonrunComparisonGUIrunComparisonShinyrunDiffExpsqrtcpm.limma.createRmdsummarizeSyntheticDataSetTCC.createRmdttest.createRmdvoom.limma.createRmdvoom.ttest.createRmd

Dependencies:apebase64encbitopsbslibcachemcaToolscliclueclustercodetoolscolorspacecommonmarkcrayondigestedgeRevaluatefansifarverfastmapfBasicsfontawesomefsfuturefuture.applyggplot2globalsgluegplotsgssgtablegtoolshighrhtmltoolshttpuvisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelifecyclelimmalistenvlocfitmagrittrmarkdownMASSMatrixmatrixStatsmemoisemgcvmimemodeestmunsellnlmeparallellyphylolmpillarpkgconfigpromisesR6rappdirsRColorBrewerRcpprlangrmarkdownrmutilROCRrpartsassscalesshinyshinydashboardsmsourcetoolsspatialstablestablediststatipstatmodstringistringrtibbletimeDatetimeSeriestinytexutf8vctrsvioplotviridisLitewithrxfunxtableyamlzoo

Comparing methods for differential expression analysis of RNAseq data with the compcodeR package

Charlotte Soneson

Rendered fromcompcodeR.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2020-09-28
Started: 2019-12-02

Including inter-species measurements in differential expression analysis of RNAseq data with the compcodeR package

Paul Bastide & Mélina Gallopin

Rendered fromphylocompcodeR.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2022-01-24
Started: 2022-01-24

Readme and manuals

Help Manual

Help pageTopics
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methodscompcodeR-package compcodeR
Check the validity of a 'compData' objectcheck_compData
Check the validity of a 'compData' result objectcheck_compData_results
Check the validity of a 'phyloCompData' objectcheck_phyloCompData
Check a list or a 'compData' object for compatibility with the differential expression functions interfaced by 'compcodeR'checkDataObject
Check consistency of input table to 'runComparison'checkTableConsistency
Create a 'compData' objectcompData
Class compDatacompData-class
Convert a 'compData' object to a listconvertcompDataToList
Convert a list with data and results to a 'compData' objectconvertListTocompData
Convert a list with data and results to a 'phyloCompData' objectconvertListTophyloCompData
Convert a 'phyloCompData' object to a listconvertphyloCompDataToList
Generate a '.Rmd' file containing code to perform differential expression analysis with DESeq2DESeq2.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with DESeq2 with custom model matrixDESeq2.length.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with DSSDSS.createRmd
Generate a .Rmd file containing code to perform differential expression analysis with EBSeqEBSeq.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with the edgeR exact testedgeR.exact.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with the edgeR GLM approachedgeR.GLM.createRmd
Generate HTML file(s) containing code used to run differential expression analysis.generateCodeHTMLs
Generate synthetic count data setsgenerateSyntheticData
Generate a '.Rmd' file containing code to perform differential expression analysis with length normalized counts + limmalengthNorm.limma.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with length normalized counts + SVA + limmalengthNorm.sva.limma.createRmd
List available *.createRmd functionslistcreateRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with limma after log-transforming the counts per million (cpm)logcpm.limma.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with NBPSeqNBPSeq.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with NOISeqNOISeq.prenorm.createRmd
Create a 'phyloCompData' objectphyloCompData
Class phyloCompDataphyloCompData-class
Generate a '.Rmd' file containing code to perform differential expression analysis with 'phylolm'.phylolm.createRmd
Run the performance comparison between differential expression methods.runComparison
A GUI to the main function for running the performance comparison between differential expression methods.runComparisonGUI
A shiny-based GUI to the main function for running the performance comparison between differential expression methods.runComparisonShiny
The main function to run differential expression analysisrunDiffExp
Show method for 'compData' objectshow,compData-method
Show method for 'phyloCompData' objectshow,phyloCompData-method
Generate a '.Rmd' file containing code to perform differential expression analysis with limma after square root-transforming the counts per million (cpm)sqrtcpm.limma.createRmd
Summarize a synthetic data set by some diagnostic plotssummarizeSyntheticDataSet
Generate a '.Rmd' file containing code to perform differential expression analysis with TCCTCC.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with a t-testttest.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with voom+limmavoom.limma.createRmd
Generate a '.Rmd' file containing code to perform differential expression analysis with voom+t-testvoom.ttest.createRmd