pseudo_seurat: Example 'Seurat'

In neurogenomics/scNLP: NLP for Single-cell Omics.

Example Seurat

Description

Contains pseudobulk data (mean expression per cell-type) from 11 different datasets. Mean expression matrices have been downsampled to 1,000/21,000 genes.

Usage

pseudo_seurat

Format

An object of class Seurat with 2000 rows and 801 columns.

Examples

## Not run: 
set.seed(2021)
pseudo_seurat <- scKirby::ingest_data("/Volumes/Steelix/model_celltype_conservation/merged/merged.11datasets.h5ad", output_type="Seurat", save_output = F)
### Find the most variable features within each dataset  
var_features <- FindVariableFeatures_split(pseudo_seurat, split.by = "batch", nfeatures = 4000, nfeatures_max = 2000)
pseudo_seurat <- pseudo_seurat[var_features, ]
usethis::use_data(pseudo_seurat, overwrite = T)

## End(Not run)

neurogenomics/scNLP documentation built on Oct. 8, 2024, 5:30 p.m.