v.1.3.16 -- updated citation now that there's a pre-print for this so…

…ftware The pre-print is available from bioRxiv at https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1
LieberInstitute · Apr 30, 2021 · 1fe8882 · 1fe8882
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: spatialLIBD
 Title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved
     transcriptomics data
-Version: 1.3.15
-Date: 2021-04-29
+Version: 1.3.16
+Date: 2021-04-30
 Authors@R:
     c(
     person("Leonardo", "Collado-Torres", role = c("aut", "cre"), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# spatialLIBD 1.3.16
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+* The citation information has changed now that `spatialLIBD` has a bioRxiv
+pre-print at https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1.
+
 # spatialLIBD 1.3.15
 
 SIGNIFICANT USER-VISIBLE CHANGES

diff --git a/README.md b/README.md
@@ -244,22 +244,21 @@ Please run this yourself to check for any updates on how to cite
 print(citation("spatialLIBD"), bibtex = TRUE)
 #> 
 #> Pardo B, Spangler A, Weber LM, Hicks SC, Jaffe AE, Martinowich K,
-#> Maynard KR, Collado-Torres L (2021). _spatialLIBD: an R/Bioconductor
-#> package to visualize spatially-resolved transcriptomics data_. doi:
-#> 10.18129/B9.bioc.spatialLIBD (URL:
-#> https://doi.org/10.18129/B9.bioc.spatialLIBD),
-#> https://github.com/LieberInstitute/spatialLIBD - R package version
-#> 1.3.15, <URL: http://www.bioconductor.org/packages/spatialLIBD>.
+#> Maynard KR, Collado-Torres L (2021). "spatialLIBD: an R/Bioconductor
+#> package to visualize spatially-resolved transcriptomics data."
+#> _bioRxiv_. doi: 10.1101/2021.04.29.440149 (URL:
+#> https://doi.org/10.1101/2021.04.29.440149), <URL:
+#> https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
-#>   @Manual{,
+#>   @Article{,
 #>     title = {spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data},
 #>     author = {Brenda Pardo and Abby Spangler and Lukas M. Weber and Stephanie C. Hicks and Andrew E. Jaffe and Keri Martinowich and Kristen R. Maynard and Leonardo Collado-Torres},
 #>     year = {2021},
-#>     url = {http://www.bioconductor.org/packages/spatialLIBD},
-#>     note = {https://github.com/LieberInstitute/spatialLIBD - R package version 1.3.15},
-#>     doi = {10.18129/B9.bioc.spatialLIBD},
+#>     journal = {bioRxiv},
+#>     doi = {10.1101/2021.04.29.440149},
+#>     url = {https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1},
 #>   }
 #> 
 #> Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,12 +1,6 @@
-pkgVer <- function(pkg) {
-    if (!exists("meta") || is.null(meta)) meta <- packageDescription(pkg)
-    ver <- meta$Version
-    paste0('https://github.com/LieberInstitute/', pkg, ' - R package version ', ver)
-}
-
 c(
 
-    bibentry(bibtype="manual",
+    bibentry(bibtype="article",
         title = "spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data",
         author = personList(
             as.person("Brenda Pardo"),
@@ -18,10 +12,10 @@ c(
             as.person("Kristen R. Maynard"),
             as.person("Leonardo Collado-Torres")
         ),
-        year = format(Sys.Date(), "%Y"),
-        url = "http://www.bioconductor.org/packages/spatialLIBD",
-        note = pkgVer('spatialLIBD'),
-        doi = '10.18129/B9.bioc.spatialLIBD'
+        year = 2021,
+        journal = "bioRxiv",
+        doi = "10.1101/2021.04.29.440149",
+        url = "https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1"
     ),
     bibentry(bibtype="article",
         title = "Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex",

diff --git a/inst/app/www/README.md b/inst/app/www/README.md
@@ -244,22 +244,21 @@ Please run this yourself to check for any updates on how to cite
 print(citation("spatialLIBD"), bibtex = TRUE)
 #> 
 #> Pardo B, Spangler A, Weber LM, Hicks SC, Jaffe AE, Martinowich K,
-#> Maynard KR, Collado-Torres L (2021). _spatialLIBD: an R/Bioconductor
-#> package to visualize spatially-resolved transcriptomics data_. doi:
-#> 10.18129/B9.bioc.spatialLIBD (URL:
-#> https://doi.org/10.18129/B9.bioc.spatialLIBD),
-#> https://github.com/LieberInstitute/spatialLIBD - R package version
-#> 1.3.15, <URL: http://www.bioconductor.org/packages/spatialLIBD>.
+#> Maynard KR, Collado-Torres L (2021). "spatialLIBD: an R/Bioconductor
+#> package to visualize spatially-resolved transcriptomics data."
+#> _bioRxiv_. doi: 10.1101/2021.04.29.440149 (URL:
+#> https://doi.org/10.1101/2021.04.29.440149), <URL:
+#> https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
-#>   @Manual{,
+#>   @Article{,
 #>     title = {spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data},
 #>     author = {Brenda Pardo and Abby Spangler and Lukas M. Weber and Stephanie C. Hicks and Andrew E. Jaffe and Keri Martinowich and Kristen R. Maynard and Leonardo Collado-Torres},
 #>     year = {2021},
-#>     url = {http://www.bioconductor.org/packages/spatialLIBD},
-#>     note = {https://github.com/LieberInstitute/spatialLIBD - R package version 1.3.15},
-#>     doi = {10.18129/B9.bioc.spatialLIBD},
+#>     journal = {bioRxiv},
+#>     doi = {10.1101/2021.04.29.440149},
+#>     url = {https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1},
 #>   }
 #> 
 #> Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams

diff --git a/man/spatialLIBD-package.Rd b/man/spatialLIBD-package.Rd
diff --git a/vignettes/TenX_data_download.Rmd b/vignettes/TenX_data_download.Rmd
@@ -15,7 +15,7 @@ author:
     - *libd
     - &ccb Center for Computational Biology, Johns Hopkins University
     email: lcolladotor@gmail.com
-output: 
+output:
   BiocStyle::html_document:
     self_contained: yes
     toc: true
@@ -26,8 +26,8 @@ date: "`r doc_date()`"
 package: "`r pkg_ver('spatialLIBD')`"
 vignette: >
   %\VignetteIndexEntry{Using spatialLIBD with 10x Genomics public datasets}
-  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}  
+  %\VignetteEngine{knitr::rmarkdown}
 ---
 
 ```{r setup, include = FALSE}
@@ -213,7 +213,7 @@ If you have the GTF file from 10x Genomics, we show next how you can read the in
 ```{r "use_10x_gtf", eval = FALSE}
 ## You could:
 ## * download the 11 GB file from
-##https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
+## https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
 ## * decompress it
 
 ## Read in the gene information from the annotation GTF file provided by 10x