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