This repository hosts code (primarily R and Python scripts) and data related to the maize developmental atlas dataset.

Repository architecture:

• snk/: pipeline scripts (snakemake and python)
• src/: data processing, statistical testing, visualization (R)
• Rmd/: figure and table typesetting (R markdown)
• README.md: (this file)

Demo datasets and scripts to:

• obtain allele specific read counts
• cis_trans.R: Classify cis/trans inheritance pattern using inbred/hybrid expression, in basic mode or differential mode

    $ ./cis_trans.R -h
    usage: ./cis_trans.R [-h] [--mode MODE] [--min_rc MIN_RC] [--n_cpu N_CPU]
                         f_rc f_sf f_dsp fo
  
    Classify cis/trans inheritance pattern using inbred/hybrid RNA-Seq read counts
  
    positional arguments:
      f_rc             read count table
      f_sf             sample-wise size factor table
      f_dsp            gene-wise dispersion table
      fo               output file
  
    optional arguments:
      -h, --help       show this help message and exit
      --mode MODE      cis/trans test mode, "basic" for steady-state cis/trans
                       test and "diff" for control/treatment differential test
                       [default: basic]
      --min_rc MIN_RC  minimum read counts to filter low-expressed genes [default:
                       10]
      --n_cpu N_CPU    number of CPUs / threads to use for parallel processing
                       (for spped up if you have many genes) [default: 1]
  

Here are links to a list of useful R scripts:

• normalize raw read counts using TMM approach
• generate sample QC statistics, PCA, hierarchical clustering, etc.
• run DE tests using DESeq2 or edgeR