Package: ideal 2.1.0

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:Federico Marini [aut, cre]

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

# 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

On BioConductor:ideal-1.99.0(bioc 3.20)ideal-1.28.0(bioc 3.19)

immunooncology geneexpression differentialexpression rnaseq sequencing visualization qualitycontrol gui genesetenrichment reportwriting shinyapps bioconductor differential-expression reproducible-research rna-seq rna-seq-analysis shiny user-friendly

6.72 score 29 stars 5 scripts 254 downloads 1 mentions 11 exports 225 dependencies

Last updated 23 days agofrom:0bd3ed6ede. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 24 2024
R-4.3-mac	NOTE	Oct 24 2024

Exports:deseqresult2DEgenes deseqresult2tbl ggplotCounts goseqTable ideal plot_ma plot_volcano read_gmt sepguesser sig_heatmap wrapup_for_iSEE

Dependencies:abind annotate AnnotationDbi AnnotationForge ape aplot askpass assertthat base64enc BH BiasedUrn Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib ca cachem callr Category caTools cli cluster clusterProfiler codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend DESeq2 digest DOSE dplyr DT egg enrichplot evaluate fansi farver fastmap fastmatch fdrtool fgsea filelock fontawesome foreach formatR fs futile.logger futile.options gclus genefilter geneLenDataBase generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggforce ggfun ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim goseq GOstats gplots graph gridExtra gridGraphics GSEABase gson gtable gtools heatmaply highr hms htmltools htmlwidgets httpuv httr httr2 igraph IHW IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit lpsymphony magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime mosdef munsell nlme openssl patchwork permute pheatmap pillar pkgconfig plogr plotly plyr png polyclip prettyunits processx progress promises ps purrr qap qvalue R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl registry rentrez reshape2 restfulr Rgraphviz Rhtslib rintrojs rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales scatterpie seriation shiny shinyAce shinyBS shinydashboard slam snow sourcetools SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidyr tidyselect tidytree tinytex topGO treeio TSP tweenr txdbmaker UCSC.utils UpSetR utf8 vctrs vegan viridis viridisLite webshot withr xfun XML xml2 xtable XVector yaml yulab.utils zlibbioc

ideal User's Guide

Federico Marini, Harald Binder

Rendered fromideal-usersguide.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-09-20
Started: 2017-01-06

Citation

Development and contributors

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