Getting started | Introduction | Citation info | Using the application | Launching r Biocpkg("ideal") locally | Accessing the public instance of r Biocpkg("ideal") | Deploying to a Shiny Server | Getting to know the user interface and the functionality | The controls sidebar | App settings | Plot export settings | Quick viewer | First steps help | The task menu | The main app panels | Welcome! | Data Setup | Counts Overview | Extract Results | Summary Plots | Gene Finder | Functional Analysis | Signatures Explorer | Report Editor | About | Running r Biocpkg("ideal") on an exemplary data set | Coming from edgeR/limma-voom | Functions exported by the package for standalone usage | deseqresult2DEgenes and deseqresult2tbl | ggplotCounts | goseqTable | plot_ma | plot_volcano | sepguesser | Creating and sharing output objects | Expanding the analysis after ideal | Enhancing ideal | Further development | Session Info
Package: ideal 2.7.0
Federico Marini
ideal: Interactive Differential Expression AnaLysis
This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.
Authors:
ideal_2.7.0.tar.gz
ideal_2.7.0.zip(r-4.7)ideal_2.7.0.zip(r-4.6)ideal_2.7.0.zip(r-4.5)
ideal_2.7.0.tgz(r-4.6-any)ideal_2.7.0.tgz(r-4.5-any)
ideal_2.7.0.tar.gz(r-4.7-any)ideal_2.7.0.tar.gz(r-4.6-any)
ideal_2.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ideal/json (API)
| # Install 'ideal' in R: |
| install.packages('ideal', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/federicomarini/ideal/issues
Pkgdown/docs site:https://federicomarini.github.io
On BioConductor:ideal-2.7.0(bioc 3.24)ideal-2.6.0(bioc 3.23)
immunooncologygeneexpressiondifferentialexpressionrnaseqsequencingvisualizationqualitycontrolguigenesetenrichmentreportwritingshinyappsbioconductordifferential-expressionreproducible-researchrna-seqrna-seq-analysisshinyuser-friendly
Last updated from:00bc48cb7b. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 370 | ||
| linux-devel-x86_64 | NOTE | 678 | ||
| source / vignettes | OK | 540 | ||
| linux-release-x86_64 | NOTE | 718 | ||
| macos-release-arm64 | NOTE | 421 | ||
| macos-oldrel-arm64 | NOTE | 397 | ||
| windows-devel | NOTE | 595 | ||
| windows-release | NOTE | 688 | ||
| windows-oldrel | NOTE | 802 | ||
| wasm-release | OK | 317 |
Exports:deseqresult2DEgenesdeseqresult2tblggplotCountsgoseqTableidealplot_maplot_volcanoread_gmtsepguessersig_heatmapwrapup_for_iSEE
Dependencies:abindaisdkannotateAnnotationDbiAnnotationForgeapeaplotaskpassassertthatbase64encBHBiasedUrnBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrCategorycaToolscigarillocliclusterclusterProfilercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestDOSEdplyrDTeggenrichitenrichplotevaluatefarverfastmapfdrtoolfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgclusgdtoolsgenefiltergeneLenDataBasegenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgoseqGOstatsgplotsgraphgridExtragridGraphicsGSEABasegsongtablegtoolsheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIHWIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitlpsymphonymagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemosdefnlmeopensslotelpatchworkpermutepheatmappillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqapqvalueR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRCurlregistryrentrezreshape2restfulrRgraphvizRhtslibrintrojsrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscatterpieSeqinfoseriationshinyshinyAceshinyBSshinydashboardslamsnowsourcetoolsSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidydrtidyrtidyselecttidytreetinytextopGOtreeioTSPtweenrtxdbmakerUCSC.utilsUpSetRutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2xtableXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Deprecated functions in ideal | deprecated |
| Generate a tidy table with the DE genes from the results of DESeq | deseqresult2DEgenes |
| Generate a tidy table with the results of DESeq | deseqresult2tbl |
| Plot normalized counts for a gene | ggplotCounts |
| Extract functional terms enriched in the DE genes, based on goseq | goseqTable |
| ideal: Interactive Differential Expression Analysis | ideal |
| ideal: Interactive Differential Expression Analysis | ideal-package ideal-pkg |
| MA-plot from base means and log fold changes | plot_ma |
| Volcano plot for log fold changes and log p-values | plot_volcano |
| Read in a GMT file | read_gmt |
| Make an educated guess on the separator character | sepguesser |
| Plot a heatmap of the gene signature on the data | sig_heatmap |
| wrapup_for_iSEE | wrapup_for_iSEE |
