v1.41.1 -- attempt to fix issue with edgeR citations

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: regionReport
 Type: Package
 Title: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
-Version: 1.41.0
-Date: 2021-11-22
+Version: 1.41.1
+Date: 2025-01-14
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
     = "[email protected]", comment = c(ORCID = "0000-0003-2140-308X")),
     person(c("Andrew", "E."), "Jaffe", role = "aut",

R/DESeq2Report.R

@@ -228,7 +228,6 @@ DESeq2Report <- function(
         DESeq2 = citation("DESeq2"),
         edgeR1 = if (isEdgeR) citation("edgeR")[1] else NULL,
         edgeR2 = if (isEdgeR) citation("edgeR")[2] else NULL,
-        edgeR6 = if (isEdgeR) RefManageR::BibEntry("inbook", key = "edgeR6", author = "Chen, Yunshun and Lun, Aaron T. L. and Smyth, Gordon K.", title = "Differential expression analysis of complex RNA-seq experiments using edgeR", booktitle = "Statistical Analysis of Next Generation Sequencing Data", year = 2014, editor = "Datta, Somnath and Nettleton, Dan", publisher = "Springer", location = "New York", pages = "51-74") else NULL,
         other = if (!software %in% c("DESeq2", "edgeR")) citation(software)[1] else NULL
     )
 

inst/DESeq2Exploration/DESeq2Exploration.Rmd

@@ -24,7 +24,7 @@ Project: `r project`.
 
 # Introduction
 
-This report is meant to help explore `r software` `r if(software == 'edgeR') Citep(bib[[c('edgeR1', 'edgeR2', 'edgeR6')]]) else if (software == 'DESeq2') Citep(bib[['DESeq2']]) else Citep(bib[['other']])` results and was generated using the `regionReport` `r Citep(bib[['regionReport']])` package. While the report is rich, it is meant to just start the exploration of the results and exemplify some of the code used to do so. If you need a more in-depth analysis for your specific data set you might want to use the `customCode` argument. This report is based on the vignette of the `DESeq2` `r Citep(bib[['DESeq2']])` package which you can find [here](http://www.bioconductor.org/packages/DESeq2).
+This report is meant to help explore `r software` `r if(software == 'edgeR') Citep(bib[c('edgeR1', 'edgeR2')]) else if (software == 'DESeq2') Citep(bib[['DESeq2']]) else Citep(bib[['other']])` results and was generated using the `regionReport` `r Citep(bib[['regionReport']])` package. While the report is rich, it is meant to just start the exploration of the results and exemplify some of the code used to do so. If you need a more in-depth analysis for your specific data set you might want to use the `customCode` argument. This report is based on the vignette of the `DESeq2` `r Citep(bib[['DESeq2']])` package which you can find [here](http://www.bioconductor.org/packages/DESeq2).
 
 ## Code setup
 
@@ -308,7 +308,7 @@ plotMDS(dge)
 
 # Reproducibility
 
-The input for this report was generated with `r software` `r if(software == 'edgeR') Citep(bib[[c('edgeR1', 'edgeR2', 'edgeR6')]]) else if (software == 'DESeq2') Citep(bib[['DESeq2']]) else Citep(bib[['other']])` `r if(software == 'DESeq2') paste('using version', metadata(dds)$version)` and the resulting features were called significantly differentially expressed if their `r elementMetadata(res)$description[grep('adjusted', elementMetadata(res)$description)]` were less than `alpha` = `r metadata(res)$alpha`. This report was generated in path `r tmpdir` using the following call to `r ifelse(software != 'edgeR', 'DESeq2Report()', 'edgeReport()')`:
+The input for this report was generated with `r software` `r if(software == 'edgeR') Citep(bib[c('edgeR1', 'edgeR2')]) else if (software == 'DESeq2') Citep(bib[['DESeq2']]) else Citep(bib[['other']])` `r if(software == 'DESeq2') paste('using version', metadata(dds)$version)` and the resulting features were called significantly differentially expressed if their `r elementMetadata(res)$description[grep('adjusted', elementMetadata(res)$description)]` were less than `alpha` = `r metadata(res)$alpha`. This report was generated in path `r tmpdir` using the following call to `r ifelse(software != 'edgeR', 'DESeq2Report()', 'edgeReport()')`:
 
 ```{r thecall, echo=FALSE}
 theCall

regionReport.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: b64e3ac5-5875-4d48-ab60-8bfae97c73da
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

vignettes/regionReport.Rmd

@@ -102,21 +102,12 @@ bib <- c(
     DESeq2 = citation("DESeq2")[1],
     edgeR1 = citation("edgeR")[1],
     edgeR2 = citation("edgeR")[2],
-    edgeR6 = RefManageR::BibEntry("inbook",
-        key = "edgeR6",
-        author = "Chen, Yunshun and Lun, Aaron T. L. and Smyth, Gordon K.",
-        title = "Differential expression analysis of complex RNA-seq experiments using edgeR",
-        booktitle = "Statistical Analysis of Next Generation Sequencing Data",
-        year = 2014,
-        editor = "Datta, Somnath and Nettleton, Dan", publisher = "Springer",
-        location = "New York", pages = "51-74"
-    ),
     DEFormats = citation("DEFormats")[1]
 )
 ```
 
 
-`r Biocpkg('regionReport')` `r Citep(bib[['regionReport']])` creates HTML or PDF reports for a set of genomic regions such as `r Biocpkg('derfinder')` `r Citep(bib[['derfinder']])` results or for feature-level analyses performed with `r Biocpkg('DESeq2')` `r Citep(bib[['DESeq2']])` or `r Biocpkg('edgeR')` `r Citep(bib[[c('edgeR1', 'edgeR2', 'edgeR6')]])`. The HTML reports are styled with `r CRANpkg('rmarkdown')` `r Citep(bib[['rmarkdown']])` by default but can optionally be styled with `r CRANpkg('knitrBootstrap')` `r Citep(bib[['knitrBootstrap']])`.
+`r Biocpkg('regionReport')` `r Citep(bib[['regionReport']])` creates HTML or PDF reports for a set of genomic regions such as `r Biocpkg('derfinder')` `r Citep(bib[['derfinder']])` results or for feature-level analyses performed with `r Biocpkg('DESeq2')` `r Citep(bib[['DESeq2']])` or `r Biocpkg('edgeR')` `r Citep(bib[c('edgeR1', 'edgeR2')])`. The HTML reports are styled with `r CRANpkg('rmarkdown')` `r Citep(bib[['rmarkdown']])` by default but can optionally be styled with `r CRANpkg('knitrBootstrap')` `r Citep(bib[['knitrBootstrap']])`.
 
 
 This package includes a basic exploration for a general set of genomic regions which can be easily customized to include the appropriate conclusions and/or further exploration of the results. Such a report can be generated using `renderReport()`. `r Biocpkg('regionReport')` has a separate template for running a basic exploration analysis of `r Biocpkg('derfinder')` 
@@ -357,7 +348,7 @@ This package was made possible thanks to:
 * `r Biocpkg('derfinderPlot')` `r Citep(bib[['derfinderPlot']])`
 * `r Biocpkg('DESeq2')` `r Citep(bib[['DESeq2']])`
 * `r CRANpkg('DT')` `r Citep(bib[['DT']])`
-* `r Biocpkg('edgeR')` `r Citep(bib[[c('edgeR1', 'edgeR2', 'edgeR6')]])`
+* `r Biocpkg('edgeR')` `r Citep(bib[c('edgeR1', 'edgeR2')])`
 * `r Biocpkg('GenomeInfoDb')` `r Citep(bib[['GenomeInfoDb']])`
 * `r Biocpkg('GenomicRanges')` `r Citep(bib[['GenomicRanges']])`
 * `r Biocpkg('ggbio')` `r Citep(bib[['ggbio']])`