Package: ideal 1.29.0

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.

Authors:Federico Marini [aut, cre]

ideal_1.29.0.tar.gz
ideal_1.29.0.zip(r-4.5)ideal_1.29.0.zip(r-4.4)ideal_1.29.0.zip(r-4.3)
ideal_1.29.0.tgz(r-4.4-any)ideal_1.29.0.tgz(r-4.3-any)
ideal_1.29.0.tar.gz(r-4.5-noble)ideal_1.29.0.tar.gz(r-4.4-noble)
ideal_1.29.0.tgz(r-4.4-emscripten)ideal_1.29.0.tgz(r-4.3-emscripten)
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-1.29.0(bioc 3.20)ideal-1.28.0(bioc 3.19)

bioconductor-package

11 exports 1.31 score 201 dependencies 1 mentions

Last updated 2 months agofrom:2541b747cd

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

Dependencies:abind annotate AnnotationDbi AnnotationForge askpass assertthat base64enc BH BiasedUrn Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob bslib ca cachem callr Category caTools cli cluster codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend DESeq2 digest doParallel dplyr DT egg evaluate fansi farver fastmap fdrtool filelock fontawesome foreach formatR fs futile.logger futile.options gclus genefilter geneLenDataBase generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel glue GO.db goseq GOstats gplots graph gridBase gridExtra GSEABase 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 munsell nlme NMF openssl pcaExplorer permute pheatmap pillar pkgconfig plogr plotly plyr png prettyunits processx progress promises ps purrr qap R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RCurl registry rentrez reshape2 restfulr Rgraphviz Rhtslib rintrojs rjson rlang rmarkdown rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales seriation shiny shinyAce shinyBS shinydashboard slam snow sourcetools SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys threejs tibble tidyr tidyselect tinytex topGO TSP txdbmaker UCSC.utils UpSetR utf8 vctrs vegan viridis viridisLite webshot withr xfun XML xml2 xtable XVector yaml zlibbioc

ideal User's Guide

Federico Marini, Harald Binder

Rendered fromideal-usersguide.Rmdusingknitr::rmarkdownon Jul 05 2024.

Last update: 2023-04-12
Started: 2017-01-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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