DEAR-OWL validation scripts and data

This design allows the workflows to be executed immediately without requiring complex relative directory path configurations. Users can easily identify and utilize the datasets based on the following standardized file naming conventions:</p><p><br></p><ul> <li><strong>Execution & Processing Scripts:</strong> <ul> <li><code>validation_script.txt</code>: The primary shell one-liner script used to automate the sequential processing, file renaming, and tool executions.</li> <li><code>*.py</code>: Python scripts responsible for statistical analysis and generating performance/consensus plots (called internally by the shell script).</li> </ul> </li> <li><strong>DEAR-OWL Output Lists:</strong> <ul> <li><code>uploaded*.csv</code>: The DEG consensus lists containing fold-change values and p-values exported from DEAR-OWL.

Files derived from the lightweight engine are explicitly distinguished by the suffix <code>_edgeR-like.csv</code>.</li> </ul> </li> <li><strong>Sequence Data (FASTA):</strong> <ul> <li><code>uploaded*.fa</code>: The 500-bp upstream promoter sequences corresponding to the target DEG lists.</li> </ul> </li> <li><strong>Reference DEG Datasets:</strong> <ul> <li><code>*brushed*.txt</code>: Reference DEG lists previously identified and published in Yoon et al. (2024, <em>Plant Physiol Biochem</em>).</li> <li><code>PRJNA*.txt</code>: Reference DEG lists corresponding to the <em>Cenchrus americanus</em> samples from Qazi et al. (2025, <em>Biosci Biotechnol Biochem</em>), also archived in Tsugama et al. (2024, Figshare).</li> </ul> </li> <li><strong>HOMER Analysis Outputs:</strong> <ul> <li><code>Homer*</code> (Directories/Folders): Output directories containing the definitive motif discovery tables, enrichment scores, and sequence logos generated by the HOMER suite.</li> </ul> </li> <li><strong>Intermediate and Outcome Files:</strong> <ul> <li>Other <code>*.png</code>, <code>*.txt</code>, and miscellaneous formats represent the raw input matrices, mid-stage transformation records, and definitive output results.</li> </ul> </li></ul><p><br></p><p>The specific genetic background, treatment conditions, and sample identifiers (e.g., QM2, VIP1-GFP) are explicitly included in the prefix of each respective filename for clear cross-referencing.</p>