Package: DEGreport 1.41.1

Lorena Pantano

DEGreport: Report of DEG analysis

Creation of ready-to-share figures of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

Authors:Lorena Pantano [aut, cre], John Hutchinson [ctb], Victor Barrera [ctb], Mary Piper [ctb], Radhika Khetani [ctb], Kenneth Daily [ctb], Thanneer Malai Perumal [ctb], Rory Kirchner [ctb], Michael Steinbaugh [ctb], Ivo Zeller [ctb]

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

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

Peer review:

Bug tracker:https://github.com/lpantano/degreport/issues

Datasets:
  • geneInfo - Data.frame with chromose information for each gene
  • humanGender - DGEList object for DE genes betwen Male and Females

On BioConductor:DEGreport-1.41.0(bioc 3.20)DEGreport-1.40.0(bioc 3.19)

bioconductor-package

32 exports 1.69 score 110 dependencies 1 dependents 6 mentions

Last updated 12 days agofrom:5c5ca55254

Exports:as.DEGSetcreateReportdegdegCheckFactorsdegColorsdegCompsdegCorCovdegCorrectdegCovariatesdegDefaultdegFilterdegMAdegMBdegMDSdegMeandegMVdegObjdegPatternsdegPCAdegPlotdegPlotClusterdegPlotWidedegQCdegResultsDEGSetdegSignaturedegSummarydegVardegVBdegVolcanogeom_corsignificants

Dependencies:abindALLaskpassbackportsBHBiobaseBiocGenericsBiocParallelbroomcirclizecliclueclustercodetoolscolorspaceComplexHeatmapConsensusClusterPluscowplotcpp11crayoncurlDelayedArraydendextendDESeq2digestdoParalleldplyredgeRevaluatefansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggdendroggplot2ggrepelGlobalOptionsglueGPArotationgridExtragtablehighrhttrIRangesisobanditeratorsjsonliteknitrlabelinglambda.rlatticelifecyclelimmalocfitloggingmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemnormtmunsellnlmeopensslpillarpkgconfigplyrpngpsychpurrrR6RColorBrewerRcppRcppArmadilloreshaperjsonrlangS4ArraysS4VectorsscalesshapesnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXVectoryamlzlibbioc

QC and downstream analysis for differential expression RNA-seq

Lorena Pantano

Rendered fromDEGreport.Rmdusingknitr::rmarkdownon Jun 29 2024.

Last update: 2022-06-17
Started: 2018-02-02

Readme and manuals

Help Manual

Help pageTopics
Deprecated functions in package DEGreportDEGreport-package DEGreport
Create report of RNAseq DEG anlaysiscreateReport
Method to get all table stored for an specific comparisondeg deg,DEGSet-method
Distribution of gene ratios used to calculate Size Factors.degCheckFactors
Make nice colors for metadatadegColors
Automatize the use of 'results()' for multiple comparisonsdegComps
Calculate the correlation relationshipt among all covariates in the metadata tabledegCorCov
Find correlation between pcs and covariatesdegCovariates
Method to get the default table to use.degCorrect degCorrect,DEGSet-method degDefault degDefault,DEGSet-method
Filter genes by groupdegFilter
MA-plot from base means and log fold changesdegMA
Distribution of expression of DE genes compared to the backgrounddegMB
Plot MDS from normalized count datadegMDS
Distribution of pvalues by expression rangedegMean
Integrate data comming from degPattern into one data objectdegMerge
Correlation of the standard desviation and the mean of the abundance of a set of genes.degMV
Create a deg object that can be used to plot expression values at shiny server:runGist(9930881)degObj
Make groups of genes using expression profile.degPatterns
smart PCA from count matrix datadegPCA
Plot top genes allowing more variables to color and shape pointsdegPlot
Plot clusters from degPattern function outputdegPlotCluster
Plot selected genes on a wide formatdegPlotWide
Plot main figures showing p-values distribution and mean-variance correlationdegQC
Complete report from DESeq2 analysisdegResults
DEGSetas.DEGSet as.DEGSet,data.frame-method as.DEGSet,DESeqResults-method as.DEGSet,TopTags-method DEGSet DEGSet-class
Plot gene signature for each group and signaturedegSignature
Print Summary Statistics of Alpha Level CutoffsdegSummary
Distribution of pvalues by standard desviation rangedegVar
Distribution of the standard desviation of DE genes compared to the backgrounddegVB
Create volcano plot from log2FC and adjusted pvalues data framedegVolcano
data.frame with chromose information for each genegeneInfo
Add correlation and p-value to a ggplot2 plotgeom_cor
DGEList object for DE genes betwen Male and FemaleshumanGender
Method to get the significant genessignificants significants,DEGSet-method significants,DESeqResults-method significants,list-method significants,TopTags-method