Merge the "mayling" branch to the "main" branch to address Bioconductor submission reviews (bump to ver. 0.99.2)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SEraster
 Type: Package
 Title: Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis
-Version: 0.99.1
+Version: 0.99.2
 Authors@R: 
     c(person("Gohta", "Aihara", email = "gaihara1@jh.edu", 
     role = c("aut", "cre"), 
@@ -41,12 +41,16 @@ Suggests:
     nnSVG,
     testthat (>= 3.0.0),    
     knitr,
-    rmarkdown
+    rmarkdown,
+    BiocManager,
+    MERINGUE,
+    remotes,
+    reshape2
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: 
-    R (>= 4.3.0)
+    R (>= 4.4.0)
 Imports: 
     BiocParallel,
     ggplot2,

README.md

@@ -29,15 +29,25 @@ require(remotes)
 remotes::install_github('JEFworks-Lab/SEraster')
 ```
 
+To install this package using Bioconductor, start R (version "4.4.0") and enter:
+``` r
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("SEraster")
+```
+
 ## Tutorials
 
 Introduction:
 
 -   [Formatting a SpatialExperiment Object for SEraster](https://jef.works/SEraster/articles/formatting-SpatialExperiment-for-SEraster.html)
 -   [Getting Started With SEraster](https://jef.works/SEraster/articles/getting-started-with-SEraster.html)
+- [SEraster for Spatial Variable Genes Analysis](https://jef.works/SEraster/articles/SEraster-for-SVG-analysis.html)
+- [Characterizing mPOA cell-type heterogeneity with spatial bootstrapping](https://jef.works/SEraster/articles/characterizing-mPOA-cell-type-heterogeneity.html)
 
 ## Citation
 
-Our preprint describing `SEraster` is available on *bioRxiv*:
+Our manuscript describing `SEraster` is available on *Bioinformatics*:
 
-[Aihara G. et al. (2024), "SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis", *bioRxiv*](https://doi.org/10.1101/2024.02.01.578436)
+[Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan, SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis, Bioinformatics, Volume 40, Issue 7, July 2024, btae412, https://doi.org/10.1093/bioinformatics/btae412](https://academic.oup.com/bioinformatics/article/40/7/btae412/7696710)

_pkgdown.yml

@@ -10,11 +10,14 @@ navbar:
       href: articles/install.html
     - text: "Tutorials"
       menu:
-        - text: "Introduction"
         - text: "Formatting a SpatialExperiment Object for SEraster"
           href: articles/formatting-SpatialExperiment-for-SEraster.html
         - text: "Getting Started With SEraster"
           href: articles/getting-started-with-SEraster.html
+        - text: "SEraster for Spatial Variable Genes Analysis"
+          href: articles/SEraster-for-SVG-analysis.html
+        - text: "Characterizing mPOA cell-type heterogeneity with spatial bootstrapping"
+          href: articles/characterizing-mPOA-cell-type-heterogeneity.html
     - text: "Functions"
       href: reference/index.html
     - text: "Changelog"

docs/.nojekyll

@@ -0,0 +1 @@
+