Scripts used to reproduced results represented in Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Requirments

1. Data Required
   • Genome file
     • Soybean (a2.v1)
     • Arabidopsis (v11)
   • Raw data 10x and stereo-seq data can be downloaded at CNCB data base
2. Softwares Required
   • CellRanger (Used for processing 10x raw data)
   • SAW (Used for processing stereo-seq 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)
   • scanorama (Used to implement 10X data integration)
   • harmonypy (Used to implement 10X data integration)
   • stereopy (Used for downstream analysis of stereoseq data)
   • Sctransform (Used for normalization of stereopy data)
   • muon (Used for normalization of stereopy data)
   • scVelo (Used to implement trajectory inference)
   • monocle3 (Used to implement trajectory inference)
   • cellrank (Used to implement trajectory inference)
   • diffxpy (Used to identify DEGs)
   • AUCell (Used for calculating gene set expression score)
   • pyscenic (Used for calculating gene set expression score)
   • jpy_tools (A wrapper of single-cell analysis tools, which is available here jpy_tools)
   • OrthoFinder (Used to find orthologs between arabidopsis and soybean)
   • rpy2 (Used to implement invocation of R packages in python environment)
   • clusterprofiler (Used to perform GO enrichmenth analysis)

Main steps

Preprocessing

1. Get 10X cell-gene matrix using the snakemake file
2. Get stereo-seq cell-gene matrix using the script
3. Get orthologs between arabidopsis and soybean using the script

Analysis

These jupyter files contains the scripts needed for downstream analysis. Github often fails to preview large jupyter files, so you can preview these files using nbviewer.

Others

• The processed file can be downloaded at OMIX data base
• The gene expression pattern can be explored at our website
  • If you found any bugs in our website, please reported here