inst/app/www/intro.md
In GENOM-IC-Cochin/shiny-rnaseq-viz: RNA-Seq Analysis Dashboard In Shiny
Welcome to Radish!
Radish is a GENOM'IC tool for RNA-seq exploration. It uses data processed with GENOM'IC's own RNA-seq pipeline, and allows you to interactively explore and visualise the data. It is a projet in development, so do expect things to change, even things to break (I sure hope not!). Please do some sanity checks on the results and figures provided by this app !
If you encounter any issue, or have any suggestion, don't hesitate to contact me (English or French)!
Changes in version 1.1.0 !
All filters (on p values or log Fold Change) on lists of Differentially Expressed Genes (DEGs) have been removed : as those list are False Discovery Rate (FDR)-corrected (the wikipedia page is quite complete) for multiple testing, subsetting or intersecting those lists leads to losing the FDR control.
Usage :
-
In the tutorial tab you can access a thorough tutorial on how to use the app.
-
In the Data tab, load the results.rds file, provided in the NGSXX-XX_Resultats folder given to you by GENOM'IC. Or try the app with some demo data kindly provided, by Juliette Paillet (Kroemer team, UMRS1138), from this article by Paillet et al. (raw data otherwise available from the Gene Expression Omnibus, under accession no. GSE180289).
GENOM-IC-Cochin/shiny-rnaseq-viz documentation built on Sept. 8, 2023, 4:23 p.m.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Welcome to Radish!
Radish is a GENOM'IC tool for RNA-seq exploration. It uses data processed with GENOM'IC's own RNA-seq pipeline, and allows you to interactively explore and visualise the data. It is a projet in development, so do expect things to change, even things to break (I sure hope not!). Please do some sanity checks on the results and figures provided by this app !
If you encounter any issue, or have any suggestion, don't hesitate to contact me (English or French)!
Changes in version 1.1.0 !
All filters (on p values or log Fold Change) on lists of Differentially Expressed Genes (DEGs) have been removed : as those list are False Discovery Rate (FDR)-corrected (the wikipedia page is quite complete) for multiple testing, subsetting or intersecting those lists leads to losing the FDR control.
Usage :
-
In the tutorial tab you can access a thorough tutorial on how to use the app.
-
In the Data tab, load the
results.rdsfile, provided in theNGSXX-XX_Resultatsfolder given to you by GENOM'IC. Or try the app with some demo data kindly provided, by Juliette Paillet (Kroemer team, UMRS1138), from this article by Paillet et al. (raw data otherwise available from the Gene Expression Omnibus, under accession no. GSE180289).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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