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Merge pull request #398 from scverse/preprocess-tutorial
add preprocessing tutorial with multiple examples
2 parents 7f51d21 + bd2c2b9 commit 434bb15

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‎atac/PeakVI.ipynb‎

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‎atac/PoissonVI.ipynb‎

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‎multimodal/MultiVI_tutorial.ipynb‎

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‎multimodal/totalVI.ipynb‎

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‎r/DestVI_in_R.ipynb‎

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"## Loading and processing data with Seurat"
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"```{note}\n",
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"For general pre-processing for various datatypes used by scvi-tools models, see the [preprocessing tutorial](https://docs.scvi-tools.org/en/stable/tutorials/notebooks/use_cases/preprocessing.html#spatial-transcriptomics).\n",
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"```"
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]
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},
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{
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"cell_type": "code",
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"metadata": {
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"vscode": {
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"# install.packages(\"Seurat\")\n",
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"cortex_sc_data <- readRDS(url(\"https://www.dropbox.com/s/cuowvm4vrf65pvq/allen_cortex.rds?dl=1\"))"
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{
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"data": {
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{
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"cell_type": "code",
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"cortex_sc_data <- NormalizeData(cortex_sc_data, normalization.method = \"LogNormalize\", scale.factor = 10000)\n",
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{
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"library(reticulate)\n",
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"cortex_sc_adata <- convertFormat(cortex_sc_data, from=\"seurat\", to=\"anndata\", main_layer=\"counts\", drop_single_values=FALSE)\n",
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"cortex_st_adata$obsm[\"proportions\"] <- stlvm$get_proportions()"
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"cortex_st_data[[\"predictions\"]] <- CreateAssayObject(data = t(py_to_r(cortex_st_adata$obsm$get(\"proportions\"))))"
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"ct_name <- \"L6 IT\"\n",
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"filtered_st_data <- cortex_st_data[, indices]\n",
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