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Zenodo
2026
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| Online Access: | https://doi.org/10.5281/zenodo.18839685 |
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Table of Contents:
- <h1>BulkSeq Workflow Tools – Version 0.1.1</h1> <p>BulkSeq Workflow Tools is a Python library designed to provide a structured and reproducible framework for preprocessing, quality control, normalization, and exploratory analysis of bulk RNA-seq datasets. The library addresses the critical stage of data curation, which is often the most time-consuming and error-prone step in transcriptomic workflows.</p> <p><strong>This update adds a CITATION.cff file and aligns metadata with version 0.1.1.</strong><br><strong>No functional changes were introduced.</strong></p> <h2>Citation:</h2> <p>Once published on Zenodo, please cite this release as:</p> <p>Manzone Rodriguez C., Angiolini S.C., Sotomayor C.E., Iribarren P. (2026).<br>BulkSeq Workflow Tools (Version 0.1.1). Zenodo.<br><a href="https://doi.org/10.5281/zenodo.18839685" rel="nofollow">10.5281/zenodo.18839685</a></p> <p>Concept DOI (represents all versions):<br><a href="https://doi.org/10.5281/zenodo.18829690" rel="nofollow">10.5281/zenodo.18829690</a></p> <h2>Main Features</h2> <ul> <li><strong>Modular and Flexible Architecture:</strong> Functions can be used independently or as part of automated workflows, allowing adaptation to different datasets and experimental designs.</li> <li><strong>Comprehensive Quality Control and Diagnostics:</strong> Includes replicate-aware filtering, missing value visualization, statistical tests for variance homogeneity, and exploratory data analysis tools.</li> <li><strong>Normalization and Transformation Methods:</strong> Supports CPM, FPKM, TPM, log-transformation, Z-score scaling, and DESeq2-based normalization through PyDESeq2.</li> <li><strong>Visualization Capabilities:</strong> Generates publication-ready figures for data distributions, zero-inflation, and statistical diagnostics.</li> <li><strong>Cross-Dataset Applicability:</strong> While optimized for bulk RNA-seq, the modular design allows application to other structured tabular datasets.</li> </ul> <h2>Included Resources</h2> <ul> <li>Example notebook demonstrating dataset loading, quality assessment, filtering, normalization, and comparative analyses.</li> <li>Subsampled example datasets derived from GEO dataset <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109297" rel="nofollow">GSE109297</a> for demonstration purposes.</li> <li>Example figures illustrating QC metrics, distributions, and statistical outputs.</li> </ul> <h2>Installation</h2> <div> <pre>git clone https://github.com/clarisamanzone/bulkseq_workflow_tools.git <span>cd</span> bulkseq_workflow_tools pip install -r requirements.txt</pre> <div> </div> </div> <h2>Citation:</h2> <p>Once published on Zenodo, please cite this release as:</p> <blockquote> <p>Manzone Rodriguez C., Angiolini S.C., Sotomayor C.E., Iribarren P. (2026).<br><strong>BulkSeq Workflow Tools (Version 0.1.0).</strong> Zenodo.<br><a href="https://zenodo.org/records/18829691" rel="nofollow">https://zenodo.org/records/18829691</a></p> <p><em>Concept DOI (represents all versions):</em><br><a href="https://doi.org/10.5281/zenodo.18829690" rel="nofollow">10.5281/zenodo.18829690</a>.</p> </blockquote> <p>This release provides a reproducible and adaptable toolkit for robust RNA-seq data preprocessing and analysis, facilitating structured workflows and reliable comparative evaluations of normalization strategies.</p>