Reading in Single Cell RNA-Seq data

#load in the Seurat libraries needed

library(Seurat)

## Attaching SeuratObject

library(SeuratDisk)

## Registered S3 method overwritten by 'SeuratDisk':
##   method            from  
##   as.sparse.H5Group Seurat

#reading in a .RDS format

rds_data <- readRDS('ependymal_cells.rds')

10x CellRanger .HDF5 format

hdf_data <- Read10X_h5(filename = "20k_PBMC_3p_HT_nextgem_Chromium_X_filtered_feature_bc_matrix.h5",
use.names = TRUE,
unique.features = TRUE)

#convert hdf5 to seurat

seurat_hdf5 <- CreateSeuratObject(counts = hdf_data)

#.loom files

loom_data <- Connect(filename =  'adult-hem-organs-10X-bone-marrow.loom',
  mode = 'r')

seurat_loom_data <- as.Seurat(loom_data)

## Reading in /matrix

## Warning: Duplicate feature names found, making unique

## Warning: Duplicate feature names found, making unique

## Storing /matrix as counts

## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')

## Saving /matrix to assay 'RNA'

#.h5ad format #convert AnnData object to an h5Seurat file

Convert("adata_SS2_for_download.h5ad", dest = "h5seurat")

## Warning: Unknown file type: h5ad

## Warning: 'assay' not set, setting to 'RNA'

## Creating h5Seurat file for version 3.1.5.9900

## Adding X as scale.data

## Adding raw/X as data

## Adding raw/X as counts

## Adding meta.features from raw/var

## Merging n_cells-0 from scaled feature-level metadata

## Merging n_cells-1 from scaled feature-level metadata

## Merging n_cells-2 from scaled feature-level metadata

## Merging n_cells-3 from scaled feature-level metadata

#Load h5Seurat file into a Seurat object

seurat_anndata <-LoadH5Seurat("adata_SS2_for_download.h5seurat")

## Validating h5Seurat file

## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')

## Initializing RNA with data

## Adding counts for RNA

## Adding scale.data for RNA

## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')

## Adding feature-level metadata for RNA

## Adding command information

## Adding cell-level metadata

## Adding miscellaneous information

## Adding tool-specific results