add helper script for conversion to h5ad #1 and update README accordi…

…ngly

README.md

@@ -187,6 +187,9 @@ Beyond this the workflow was tested on multimodal scCRISPR-seq data sets with >3
 - [Snakemake Workflow Catalog Entry](https://snakemake.github.io/snakemake-workflow-catalog?usage=epigen/scrnaseq_processing_seurat)
 
 # 📚 Resources
+- Helper scripts
+  - [Converting Parse Bioscience scRNA-seq data to (expected) 10x Genomics/MTX format](./helpers/parse_to_10x_conversion.R)
+  - [Converting Seurat object to scanpy compatible anndata object in `h5ad` format](./helpers/Seurat_to_h5ad_conversion.R)
 - Data Resources for scRNA-seq data in compatible MTX format
   - [10X Genomics Datasets](https://www.10xgenomics.com/datasets)
   - [CELLxGENE](https://cellxgene.cziscience.com/)

helpers/Seurat_to_h5ad_conversion.R

@@ -0,0 +1,19 @@
+# adapted from: https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html
+
+# libraries
+library("Seurat")
+library("SeuratDisk")
+
+# configs
+object_path <- file.path("path/to/Seurat/object.rds")
+results_path <- file.path("result/path")
+dir.create(results_path, recursive = TRUE)
+
+# load seurat object
+data <- readRDS(file = file.path(object_path))
+
+# save as h5Seurat
+SaveH5Seurat(data, filename = file.path(results_path,"object.h5Seurat"), overwrite = TRUE)
+
+# convert to anndata for scanpy (https://mojaveazure.github.io/seurat-disk/reference/Convert.html)
+Convert(file.path(results_path,"object.h5Seurat"), assay = "SCT", dest = "h5ad", overwrite = TRUE)