Package: DeeDeeExperiment 1.3.0

Najla Abassi

DeeDeeExperiment: DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results

DeeDeeExperiment is an S4 class extending the SingleCellExperiment class, designed to integrate and manage omics analysis results. It introduces two dedicated slots to store Differential Expression Analysis (DEA) results and Functional Enrichment Analysis (FEA) results, providing a structured approach for downstream analysis.

Authors:Najla Abassi [aut, cre], Lea Schwarz [aut], Federico Marini [aut]

DeeDeeExperiment_1.3.0.tar.gz
DeeDeeExperiment_1.3.0.zip(r-4.7)DeeDeeExperiment_1.3.0.zip(r-4.6)DeeDeeExperiment_1.3.0.zip(r-4.5)
DeeDeeExperiment_1.3.0.tgz(r-4.6-any)DeeDeeExperiment_1.3.0.tgz(r-4.5-any)
DeeDeeExperiment_1.3.0.tar.gz(r-4.7-any)DeeDeeExperiment_1.3.0.tar.gz(r-4.6-any)
DeeDeeExperiment_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DeeDeeExperiment/json (API)
NEWS

# Install 'DeeDeeExperiment' in R:

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

Bug tracker:https://github.com/imbeimainz/deedeeexperiment/issues

Datasets:

clusterPro_res - 'clusterPro_res'
de_limma - A sample 'MArrayLM' object
de_named_list - De_named_list
dge_exact_IFNg_both - A sample 'DGEExact' object
dge_exact_IFNg_naive - A sample 'DGEExact' object
dge_exact_Salm_both - A sample 'DGEExact' object
dge_exact_Salm_naive - A sample 'DGEExact' object
dge_lrt_IFNg_both - A sample 'DGELRT' object
dge_lrt_IFNg_naive - A sample 'DGELRT' object
dge_lrt_Salm_both - A sample 'DGELRT' object
dge_lrt_Salm_naive - A sample 'DGELRT' object
enrichr_res - 'enrichr_res'
fgseaRes - 'fgseaRes'
gost_res - 'gost_res'
gsea_res - 'gsea_res'
IFNg_both - A sample 'DESeqResults' object
IFNg_naive - A sample 'DESeqResults' object
muscat_res - 'muscat_res'
Salm_both - A sample 'DESeqResults' object
Salm_naive - A sample 'DESeqResults' object
topGO_results_list - 'topGO_results_list'

On BioConductor:DeeDeeExperiment-1.3.0(bioc 3.24)DeeDeeExperiment-1.2.0(bioc 3.23)

software infrastructure datarepresentation geneexpression transcription transcriptomics differentialexpression pathways go

4.20 score 1 scripts 184 downloads 24 exports 51 dependencies

Last updated from:9bf542794e. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	337
linux-devel-x86_64	WARNING	489
source / vignettes	ERROR	502
linux-release-x86_64	WARNING	546
macos-release-arm64	WARNING	220
macos-oldrel-arm64	WARNING	301
windows-devel	WARNING	522
windows-release	WARNING	482
windows-oldrel	WARNING	423
wasm-release	OK	272

Exports:addDEA addFEA addScenarioInfo DeeDeeExperiment export_result_for_dde getDEA getDEAInfo getDEAInfo<-getDEAList getDEANames getFEA getFEAInfo getFEAInfo<-getFEAList getFEANames limma_list_for_dde linkDEAandFEA muscat_list_for_dde removeDEA removeFEA renameDEA renameFEA show supported_fea_formats

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 Matrix MatrixGenerics matrixStats R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray statmod SummarizedExperiment vctrs viridisLite withr writexl XVector

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'clusterPro_res'	clusterPro_res
dd_list_original	dd_list_original
A sample 'MArrayLM' object	de_limma
de_named_list	de_named_list
The DeeDeeExperiment class	.DeeDeeExperiment DeeDeeExperiment DeeDeeExperiment-class
Methods for DeeDeeExperiment objects	addDEA addDEA,DeeDeeExperiment-method addFEA addFEA,DeeDeeExperiment-method addScenarioInfo addScenarioInfo,DeeDeeExperiment-method DeeDeeExperiment-methods getDEA getDEA,DeeDeeExperiment-method getDEAInfo getDEAInfo,DeeDeeExperiment-method getDEAInfo<- getDEAInfo<-,DeeDeeExperiment-method getDEAList getDEAList,DeeDeeExperiment-method getDEANames getDEANames,DeeDeeExperiment-method getFEA getFEA,DeeDeeExperiment-method getFEAInfo getFEAInfo,DeeDeeExperiment-method getFEAInfo<- getFEAInfo<-,DeeDeeExperiment-method getFEAList getFEAList,DeeDeeExperiment-method getFEANames getFEANames,DeeDeeExperiment-method linkDEAandFEA linkDEAandFEA,DeeDeeExperiment-method removeDEA removeDEA,DeeDeeExperiment-method removeFEA removeFEA,DeeDeeExperiment-method renameDEA renameDEA,DeeDeeExperiment-method renameFEA renameFEA,DeeDeeExperiment-method
Miscellaneous DeeDeeExperiment methods	DeeDeeExperiment-misc show,DeeDeeExperiment-method summary,DeeDeeExperiment-method
DeeDeeExperiment	DeeDeeExperiment-package DeeDeeExperiment-pkg
A sample 'DGEExact' object	dge_exact_IFNg_both
A sample 'DGEExact' object	dge_exact_IFNg_naive
A sample 'DGEExact' object	dge_exact_Salm_both
A sample 'DGEExact' object	dge_exact_Salm_naive
A sample 'DGELRT' object	dge_lrt_IFNg_both
A sample 'DGELRT' object	dge_lrt_IFNg_naive
A sample 'DGELRT' object	dge_lrt_Salm_both
A sample 'DGELRT' object	dge_lrt_Salm_naive
'enrichr_res'	enrichr_res
Export DEA/FEA/ASSAY results from a 'DeeDeeExperiment' to excel files	export_result_for_dde
'fgseaRes'	fgseaRes
'gost_res'	gost_res
'gsea_res'	gsea_res
A sample 'DESeqResults' object	IFNg_both
A sample 'DESeqResults' object	IFNg_naive
Convert a 'MArrayLM' object with multiple contrasts into a list of DE results tables compatible with DeeDeeExperiment	limma_list_for_dde
Convert 'muscat::pbDS()' results into a flat list of data frames compatible with 'DeeDeeExperiment'	muscat_list_for_dde
'muscat_res'	muscat_res
A sample 'DESeqResults' object	Salm_both
A sample 'DESeqResults' object	Salm_naive
Display available FEA formats	supported_fea_formats
'topGO_results_list'	topGO_results_list