Reproducible scRNA-seq PBMC Workflow: Reference, Toy Demonstration Data, and Analysis Outputs
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| Format: | Recurso digital |
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2024
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| _version_ | 1866902315949096960 |
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| author | Inkala, Simo |
| author_facet | Inkala, Simo |
| contents | <p>This record contains a fully reproducible, containerized single-cell RNA-seq workflow for PBMC data analysis.</p> <p>The workflow implements:</p> <ul> <li> <p>FASTQ quality control</p> </li> <li> <p>STARsolo alignment</p> </li> <li> <p>Seurat-based QC, normalization, clustering, and annotation</p> </li> <li> <p>Pseudobulk differential expression and TOST equivalence testing</p> </li> <li> <p>Cell-type–specific co-expression network construction</p> </li> </ul> <p>Version 1 provides a lightweight demonstration bundle including:</p> <ul> <li> <p>A chromosome 1 (chr1) GRCh38 mini-reference</p> </li> <li> <p>A pre-built STAR index for chr1</p> </li> <li> <p>A reduced FASTQ subset (~100k reads) for rapid execution</p> </li> </ul> <p>This demonstration dataset is designed to run in 5–10 minutes on a standard workstation and illustrates full pipeline functionality without requiring large memory resources.</p> <p>Future versions of this record will include the full GRCh38 reference, complete STAR index, and full-scale analysis outputs.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18642101 |
| institution | Zenodo |
| language | |
| publishDate | 2024 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Reproducible scRNA-seq PBMC Workflow: Reference, Toy Demonstration Data, and Analysis Outputs Inkala, Simo Single-Cell Analysis single-cell RNA-seq PBMC STARsolo Seurat reproducible workflow Docker Snakemake <p>This record contains a fully reproducible, containerized single-cell RNA-seq workflow for PBMC data analysis.</p> <p>The workflow implements:</p> <ul> <li> <p>FASTQ quality control</p> </li> <li> <p>STARsolo alignment</p> </li> <li> <p>Seurat-based QC, normalization, clustering, and annotation</p> </li> <li> <p>Pseudobulk differential expression and TOST equivalence testing</p> </li> <li> <p>Cell-type–specific co-expression network construction</p> </li> </ul> <p>Version 1 provides a lightweight demonstration bundle including:</p> <ul> <li> <p>A chromosome 1 (chr1) GRCh38 mini-reference</p> </li> <li> <p>A pre-built STAR index for chr1</p> </li> <li> <p>A reduced FASTQ subset (~100k reads) for rapid execution</p> </li> </ul> <p>This demonstration dataset is designed to run in 5–10 minutes on a standard workstation and illustrates full pipeline functionality without requiring large memory resources.</p> <p>Future versions of this record will include the full GRCh38 reference, complete STAR index, and full-scale analysis outputs.</p> |
| title | Reproducible scRNA-seq PBMC Workflow: Reference, Toy Demonstration Data, and Analysis Outputs |
| topic | Single-Cell Analysis single-cell RNA-seq PBMC STARsolo Seurat reproducible workflow Docker Snakemake |
| url | https://doi.org/10.5281/zenodo.18642101 |