DOI

RNAseqChef

RNAseqChef, an RNA-seq data controller highlighting gene expression features, is a web-based application (https://imeg-ku.shinyapps.io/RNAseqChef/, mirror 1, mirror 2) for automated, systematic, and integrated RNA-seq differential expression analysis. RNAseqChef is designed for wet-bench scientists with little computational programming skill to dissect multiple RNA-seq datasets quickly.

Manual

Manual： https://github.com/Kan-E/RNAseqChef/wiki
Manual (Japanese)：https://kan-e.github.io/RNAseqChef_manual_japanese/

Citation

When the user publishes the results from RNAseqChef analysis, please cite our original paper. - Etoh K. & Nakao M. A web-based integrative transcriptome analysis, RNAseqChef, uncovers cell/tissue type-dependent action of sulforaphane. JBC, 299(6), 104810 (2023) https://doi.org/10.1016/j.jbc.2023.104810

Local installation

Method 1 (Docker is required)

  • Download Docker
  • Run the following commands once to get the docker image of RNAseqChef
docker pull omicschef/rnaseqchef:latest

You may now run RNAseqChef with just one command in the command line:

docker run --rm -p 3838:3838 omicschef/rnaseqchef:latest

Please access http://localhost:3838 in your browser.

Method 2 (R environment setup is required)

  • Download R and RStudio (In the case of macOS, additionally install XQuartz and Xcode)
  • Run the following commands once
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    
install.packages("https://cran.r-project.org/src/contrib/Archive/lasso2/lasso2_1.2-22.tar.gz",repos = NULL, type = "source")

pkgs <- c("shiny","DT","readxl","rstatix","multcomp","tidyverse","ggpubr","venn","ggrepel",
"ggdendro","ggplotify","gridExtra","cowplot","DESeq2","ggnewscale","edgeR","IHW",
"qvalue","org.Hs.eg.db","org.Mm.eg.db","org.Rn.eg.db","org.Xl.eg.db","org.Dm.eg.db",
"org.Ce.eg.db","AnnotationDbi","clusterProfiler","enrichplot","DOSE","msigdbr","genefilter",
"ComplexHeatmap","shinyBS","plotly","shinyjs","DEGreport","devtools","dorothea","umap", "biomaRt",
"monaLisa","GenomicRanges","BiocParallel","SummarizedExperiment","JASPAR2020",
"TxDb.Mmusculus.UCSC.mm10.knownGene","TxDb.Hsapiens.UCSC.hg19.knownGene",
"BSgenome.Mmusculus.UCSC.mm10","BSgenome.Hsapiens.UCSC.hg19","TFBSTools", "org.Bt.eg.db",
"org.Dr.eg.db","org.Cf.eg.db","org.Gg.eg.db","org.Mmu.eg.db","org.Pt.eg.db","org.Sc.sgd.db","org.At.tair.db","colorspace","magick","pdftools","clue")
options(repos = BiocManager::repositories())
for(pkg in pkgs) if (!require(pkg, character.only = T)){
    BiocManager::install(pkg, update = F)
}
devtools::install_github("YuLab-SMU/clusterProfiler.dplyr")
devtools::install_github('VPetukhov/ggrastr')
devtools::install_github("wiscstatman/EBSeq")

You may now run RNAseqChef with just one command in R:

shiny::runGitHub("RNAseqChef", "Kan-E")

Reference

Shiny framework

EBSeq (for ebseq)

DESeq2 (for deseq2)

edgeR (for edger)

IHW, Independent hypothesis weighting, and qvalue (for fdr control method of deseq2 and edger)

ggdendro (for dendrograms)

umap (for UMAP)

clusterProfiler, DOSE, msigdbr, dorothea (for enrichment analysis)

AnnotationDbi,org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Xl.eg.db, org.Dm.eg.db, org.Ce.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Sc.sgd.db, and org.At.tair.db (for genome wide annotation)

biomaRt (for ortholog)

genefilter (for z-score normalization)

ComplexHeatmap (for heatmap and k-means clustering)

ggplot2 and ggpubr (for boxplot and scater plot)

DEGreport (for divisive clustering analysis)

venn (for venn diagram analysis)

GenomicRanges, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Mmusculus.UCSC.mm10, and BSgenome.Hsapiens.UCSC.hg19 (for promoter sequence)

monaLisa, TFBSTools, BiocParallel, SummarizedExperiment, and JASPAR2020 (for promoter motif analysis)

dplyr and tidyr (for data manipulation)

License

This shiny code is licensed under the GPLv3. Please see the file LICENSE.md for information.

RNAseqChef, an RNA-seq data controller highlighting gene expression features
Shiny App for automated, systematic, and integrated RNA-seq differential expression analysis
Copyright (C) 2022  Kan Etoh

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

You may contact the author of this code, Kan Etoh, at <kaneto@kumamoto-u.ac.jp>

Author

Kan Etoh <kaneto@kumamoto-u.ac.jp>