Data Access
R Objects
For this human brain dataset composed of 3 Visium capture areas, the @@ -445,7 +451,7 @@
R Objects
## Download the spot-level data, which is a SpatialExperiment object spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe") #> snapshotDate(): 2024-04-29 -#> 2024-07-31 11:39:31.483266 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1 +#> 2024-07-31 12:07:32.328879 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/154352e7328f0_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1 spe #> class: SpatialExperiment #> dim: 26369 13965 @@ -475,22 +481,29 @@R Objects
)
-
+Citing Our Work
+
+
+Raw data
+The source data described in this manuscript are available from Globus
+(jhpce#visiumStitched_brain). This includes all the input
+FASTQ files as well as the outputs from SpaceRanger.
+
-Citing Our Work
Below is the citation output from using
citation('visiumStitched') in R. Please run this yourself
to check for any updates on how to cite
visiumStitched.
print(citation("visiumStitched")[2], bibtex = TRUE)
-#> Eagles NJ, Bach S, Tippani M, Du Y, Miller RA, Hyde TM, Page SC, Martinowich K, Collado-Torres L
-#> (2024). "visiumStitched." _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
+#> Eagles NJ, Bach S, Tippani M, Ravichandran P, Du Y, Miller RA, Hyde TM, Page SC, Martinowich K,
+#> Collado-Torres L (2024). "visiumStitched." _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
#> <https://www.biorxiv.org/content/10.1101/TODO>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {visiumStitched},
-#> author = {Nicholas J. Eagles and Svitlana Bach and Madhavi Tippani and Yufeng Du and Ryan A. Miller and Thomas M. Hyde and Stephanie C. Page and Keri Martinowich and Leonardo Collado-Torres},
+#> author = {Nicholas J. Eagles and Svitlana Bach and Madhavi Tippani and Prashanthi Ravichandran and Yufeng Du and Ryan A. Miller and Thomas M. Hyde and Stephanie C. Page and Keri Martinowich and Leonardo Collado-Torres},
#> year = {2024},
#> journal = {bioRxiv},
#> doi = {10.1101/TODO},
@@ -522,7 +535,6 @@ Cite spatialLIBD
#> url = {https://doi.org/10.1186/s12864-022-08601-w},
#> }