Remove zellkonverter, trouble installing anaconda with basilisk

DESCRIPTION

@@ -95,8 +95,7 @@ Suggests:
     tidyr,
     uwot,
     vdiffr,
-    vroom,
-    zellkonverter
+    vroom
 VignetteBuilder: 
     knitr
 biocViews:GeneExpression, Spatial, Transcriptomics, Visualization

vignettes/vig10_10x_nuclei.Rmd

@@ -63,17 +63,12 @@ library(SpatialFeatureExperiment)
 library(scater)
 library(scuttle)
 library(Voyager)
-library(zellkonverter)
 library(ggplot2)
 theme_set(theme_bw())
 ```
 
-```{r dwnld, message=FALSE, results='hide'}
-download.file("https://github.com/cellatlas/cellatlas/raw/main/examples/rna-10xv3-nuclei/cellatlas_out/adata.h5ad.gz", 
-                  "adata.h5ad.gz", quiet = TRUE)
-system("gunzip -f adata.h5ad.gz")
-sce <- readH5AD("adata.h5ad")
-assayNames(sce) <- "counts"
+```{r}
+sce <- readRDS("10xnuclei.rds")
 ```
 
 ```{r}

vignettes/vig11_clicktags.Rmd

@@ -64,17 +64,12 @@ library(SpatialFeatureExperiment)
 library(scater)
 library(scuttle)
 library(Voyager)
-library(zellkonverter)
 library(ggplot2)
 theme_set(theme_bw())
 ```
 
-```{r dwnld, message=FALSE, results='hide'}
-download.file("https://github.com/cellatlas/cellatlas/raw/main/examples/tag-clicktag/cellatlas_out/adata.h5ad.gz", 
-                  "adata.h5ad.gz", quiet = TRUE)
-system("gunzip -f adata.h5ad.gz")
-sce <- readH5AD("adata.h5ad")
-assayNames(sce) <- "counts"
+```{r}
+sce <- readRDS("clicktags.rds")
 ```
 
 ```{r}

vignettes/vig12_crispr.Rmd

@@ -64,16 +64,12 @@ library(SpatialFeatureExperiment)
 library(scater)
 library(scuttle)
 library(Voyager)
-library(zellkonverter)
 library(ggplot2)
 theme_set(theme_bw())
 ```
 
-```{r dwnld, message=FALSE, results='hide'}
-download.file("https://github.com/cellatlas/cellatlas/raw/main/examples/crispr-10xcrispr/cellatlas_out/adata.h5ad.gz", "adata.h5ad.gz", quiet = TRUE)
-system("gunzip -f adata.h5ad.gz")
-sce <- readH5AD("adata.h5ad")
-assayNames(sce) <- "counts"
+```{r}
+sce <- readRDS("10xcrispr.rds")
 ```
 
 ```{r}

vignettes/vig13_10xatac.Rmd

@@ -65,17 +65,11 @@ library(SpatialFeatureExperiment)
 library(scater)
 library(scuttle)
 library(Voyager)
-library(zellkonverter)
 library(ggplot2)
 theme_set(theme_bw())
 ```
-
-```{r dwnld, message=FALSE, results='hide'}
-download.file("https://github.com/cellatlas/cellatlas/raw/main/examples/atac-10xatac/cellatlas_out/adata.h5ad.gz", 
-                  "adata.h5ad.gz", quiet = TRUE)
-system("gunzip -f adata.h5ad.gz")
-sce <- readH5AD("adata.h5ad")
-assayNames(sce) <- "counts"
+```{r}
+sce <- readRDS("10xatac.rds")
 ```
 
 ```{r}

vignettes/vig14_10xmultiome.Rmd

@@ -65,17 +65,12 @@ library(SpatialFeatureExperiment)
 library(scater)
 library(scuttle)
 library(Voyager)
-library(zellkonverter)
 library(ggplot2)
 theme_set(theme_bw())
 ```
 
-```{r dwnld, message=FALSE, results='hide'}
-download.file("https://github.com/cellatlas/cellatlas/raw/main/examples/atac-10xmultiome/cellatlas_out/adata.h5ad.gz", 
-                  "adata.h5ad.gz", quiet = TRUE)
-system("gunzip -f adata.h5ad.gz")
-sce <- readH5AD("adata.h5ad")
-assayNames(sce) <- "counts"
+```{r}
+sce <- readRDS("10xmultiome.rds")
 ```
 
 ```{r}

vignettes/vig9_splitseq.Rmd

@@ -62,7 +62,6 @@ install.packages("anndata")
 The data in this vignette is shipped with the `cellatlas` repository. The count matrix and metadata are provided in the `cellatlas/examples` folder as an [`AnnData`](https://anndata-tutorials.readthedocs.io/en/latest/getting-started.html) object. We will begin by loading the object and converting it to a `SpatialFeatureExperiment` object. 
 
 ```{r setup, message=FALSE}
-library(zellkonverter)
 library(stringr)
 library(Matrix)
 library(SpatialExperiment)
@@ -72,12 +71,8 @@ library(scuttle)
 library(Voyager)
 ```
 
-```{r dwnld}
-download.file("https://github.com/cellatlas/cellatlas/raw/main/examples/rna-splitseq/cellatlas_out/adata.h5ad.gz", 
-              "adata.h5ad.gz", quiet = TRUE)
-system("gunzip -f adata.h5ad.gz")
-sce <- readH5AD("adata.h5ad")
-assayNames(sce) <- "counts"
+```{r}
+sce <- readRDS("splitseq.rds")
 ```
 
 ```{r}