Auto-encoder for data integration

Data

Seurat object from Challenge: Link
- Swarbrick_metastatic_lymphnode.seurat.Rdata is the input of 0_Prepare_data.R
Data folder (Generated by me): Link
- scProteomics.txt and scRNAseq.txt (output of 0_Prepare_data.R) are input of 1_Integrated_Data.ipynb
- autoencoder_50dim_test.csv (output of 1_Integrated_Data.ipynb) is input of 2_Cite-seq_Analysis_R.R

Workflow

Step 1: 0_Prepare_data.R
Step 2: 1_Integrated_Data.ipynb
Step 3: 2_Cite-seq_Analysis_R.R

Requirement packages:

Python: pandas, numpy, keras
R: Seurat (v3), SingleR, tidyverse