Package: DEGreport 1.49.0

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]

DEGreport_1.49.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DEGreport/json (API)

# Install 'DEGreport' in R:

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

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

Pkgdown/docs site:https://lpantano.github.io

Datasets:

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

On BioConductor:DEGreport-1.49.0(bioc 3.24)DEGreport-1.48.0(bioc 3.23)

differentialexpression visualization rnaseq reportwriting geneexpression immunooncology bioconductor differential-expression qc report rna-seq smallrna

9.74 score 29 stars 1 packages 536 scripts 1.2k downloads 6 mentions 32 exports 98 dependencies

Last updated from:9e7c3c30cd. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	207
linux-devel-x86_64	NOTE	422
source / vignettes	OK	320
linux-release-x86_64	NOTE	398
macos-release-arm64	NOTE	314
macos-oldrel-arm64	NOTE	260
windows-devel	NOTE	388
windows-release	NOTE	354
windows-oldrel	NOTE	334
wasm-release	OK	157

Exports:as.DEGSet createReport deg degCheckFactors degColors degComps degCorCov degCorrect degCovariates degDefault degFilter degMA degMB degMDS degMean degMV degObj degPatterns degPCA degPlot degPlotCluster degPlotWide degQC degResults DEGSet degSignature degSummary degVar degVB degVolcano geom_cor significants

Dependencies:abind ALL backports BH Biobase BiocGenerics BiocParallel broom circlize cli clue cluster codetools colorspace ComplexHeatmap ConsensusClusterPlus cowplot cpp11 crayon DelayedArray dendextend DESeq2 digest doParallel dplyr edgeR evaluate farver foreach formatR futile.logger futile.options generics GenomicRanges GetoptLong ggdendro ggplot2 ggrepel GlobalOptions glue GPArotation gridExtra gtable highr IRanges isoband iterators knitr labeling lambda.r lattice lifecycle limma locfit logging magrittr MASS Matrix MatrixGenerics matrixStats mnormt nlme pillar pkgconfig plyr png psych purrr R6 RColorBrewer Rcpp RcppArmadillo reshape rjson rlang S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray statmod stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr xfun XVector yaml

QC and downstream analysis for differential expression RNA-seq

Rendered fromDEGreport.Rmdusingknitr::rmarkdown

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

Help page	Topics
Deprecated functions in package DEGreport	DEGreport-package DEGreport
Create report of RNAseq DEG anlaysis	createReport
Method to get all table stored for an specific comparison	deg deg,DEGSet-method
Distribution of gene ratios used to calculate Size Factors.	degCheckFactors
Make nice colors for metadata	degColors
Automatize the use of 'results()' for multiple comparisons	degComps
Calculate the correlation relationshipt among all covariates in the metadata table	degCorCov
Find correlation between pcs and covariates	degCovariates
Method to get the default table to use.	degCorrect degCorrect,DEGSet-method degDefault degDefault,DEGSet-method
Filter genes by group	degFilter
MA-plot from base means and log fold changes	degMA
Distribution of expression of DE genes compared to the background	degMB
Plot MDS from normalized count data	degMDS
Distribution of pvalues by expression range	degMean
Integrate data comming from degPattern into one data object	degMerge
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 data	degPCA
Plot top genes allowing more variables to color and shape points	degPlot
Plot clusters from degPattern function output	degPlotCluster
Plot selected genes on a wide format	degPlotWide
Plot main figures showing p-values distribution and mean-variance correlation	degQC
Complete report from DESeq2 analysis	degResults
DEGSet	as.DEGSet as.DEGSet,data.frame-method as.DEGSet,DESeqResults-method as.DEGSet,TopTags-method DEGSet DEGSet-class
Plot gene signature for each group and signature	degSignature
Print Summary Statistics of Alpha Level Cutoffs	degSummary
Distribution of pvalues by standard desviation range	degVar
Distribution of the standard desviation of DE genes compared to the background	degVB
Create volcano plot from log2FC and adjusted pvalues data frame	degVolcano
data.frame with chromose information for each gene	geneInfo
Add correlation and p-value to a ggplot2 plot	geom_cor
DGEList object for DE genes betwen Male and Females	humanGender
Method to get the significant genes	significants significants,DEGSet-method significants,DESeqResults-method significants,list-method significants,TopTags-method

Package: DEGreport 1.49.0

DEGreport: Report of DEG analysis

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