diff --git a/DESCRIPTION b/DESCRIPTION index f2b926d1..17d95444 100644 --- 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 index 2774553a..cf7650ad 100644 --- 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 index d4ade043..c65bb656 100644 --- 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, . +#> 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), 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 index 0cf71f25..f04dd301 100644 --- 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 index b21b8f04..8cc9b5e9 100644 --- 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, . +#> 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), 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 index 847241d7..9301c13a 100644 --- a/man/spatialLIBD-package.Rd +++ b/man/spatialLIBD-package.Rd @@ -31,7 +31,7 @@ Other contributors: \item Andrew E. Jaffe \email{andrew.jaffe@libd.org} (\href{https://orcid.org/0000-0001-6886-1454}{ORCID}) [contributor] \item Brenda Pardo \email{bpardo@lcgej.unam.mx} (\href{https://orcid.org/0000-0001-8103-7136}{ORCID}) [contributor] \item Abby Spangler \email{aspangle@gmail.com} (\href{https://orcid.org/0000-0002-0028-9348}{ORCID}) [contributor] - \item Jesús Vélez \email{jvelezmagic@gmail.com} (\href{https://orcid.org/0000-0001-5128-3838}{ORCID}) [contributor] + \item Jesús Vélez Santiago \email{jvelezmagic@gmail.com} (\href{https://orcid.org/0000-0001-5128-3838}{ORCID}) [contributor] } } diff --git a/vignettes/TenX_data_download.Rmd b/vignettes/TenX_data_download.Rmd index 634c6f79..2d2d0bd6 100644 --- 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