LFF_spatial_ERC

LFF_spatial_ERC

Internal

JHPCE location: /dcs05/lieber/marmaypag/LFF_spatialERC_LIBD4140/LFF_spatial_ERC/

Interactive Websites

All of these interactive websites are powered by open source software, namely:

• 🔭 spatialLIBD
• 👀 iSEE

We provide the following interactive websites to explore the ERC data:

• 🔭 LFF_ERC_Visium: Visium data for 31 samples post-QC w/ clustering and modeling results

• 🔭 LFF_ERC_Visium_QC: Visium data for 31 samples pre-QC drops (including out-tissue spots)

• 👀 iSEE: snRNA-seq data for 31 samples

Main Data

snRNA-seq

SingleCellExperiment

project path: "processed-data/sce_objects/sce_ERC_subcluster"

JHPCE path: "/dcs05/lieber/marmaypag/LFF_spatialERC_LIBD4140/LFF_spatial_ERC/processed-data/sce_objects/sce_ERC_subcluster"

Not on github due to size (36G)

## Load HD5F sce
sce <- HDF5Array::loadHDF5SummarizedExperiment(here::here("processed-data", "sce_objects", "sce_ERC_subcluster"))
# class: SingleCellExperiment 
# dim: 38606 122004

Pseudobulked snRNA-seq

cell type fine: processed-data/08_pseudoBulkDGE_sn/01_pseudobulk_data_sn/sce_pseudo_DGE-cell_type_anno.RDS cell type broad: processed-data/08_pseudoBulkDGE_sn/01_pseudobulk_data_sn/sce_pseudo_DGE-cell_type_broad.RDS

FASTQ

raw-data/FASTQ_snRNAseq

Sample ID table processed-data/04_snRNA-seq/erc_sn_sample_info.csv

Visium

SpatialExperiment

project path: "processed-data/spe_objects/spe_ERC_annotated"

JHPCE path: /dcs05/lieber/marmaypag/LFF_spatialERC_LIBD4140/LFF_spatial_ERC/processed-data/spe_objects/spe_ERC_annotated

pre-QC version: processed-data/spe_objects/spe_raw.rds

Not on github due to size (4G)

## Load HD5F spe
spe <- HDF5Array::loadHDF5SummarizedExperiment(here::here("processed-data", "spe_objects", "spe_ERC_annotated"))
# class: SpatialExperiment 
# dim: 30494 122202 

Pseudobulked Visium data

processed-data/09_pseudoBulkDGE_Visium/01_pseudobulk_data_Visium/spe_pseudo_DGE.RDS

FASTQ

raw-data/FASTQ

Images

raw-data/FASTQ/Images

SAMPLE ID table

processed-data/02_build_spe/sample_info.csv