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:

maizeumn/atlas

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