Requirments

1. Data Required
   • Genome file
     • Medicago (v4)
   • Raw data
2. Softwares Required
   • CellRanger (Used for processing 10x raw data)
   • scanpy (Used for downstream analysis of 10X data)
   • Seurat (Used for downstream analysis of 10X data)
   • scDblFinder (Used for removing putative doublets)
   • scvi-tools (Used to implement 10X data integration)
   • diffxpy (Used to identify DEGs)
   • edgeR (Used to identify DEGs with replicates)
   • pyscenic (Used for calculating gene set expression score)
   • rpy2 (Used to implement invocation of R packages in python environment)
   • clusterprofiler (Used to perform GO enrichment analysis)

This jupyter files contains the scripts needed for downstream analysis. Github often fails to preview large jupyter files, You can preview this file using nbviewer.

The processed data can be accessed at OMIX database