Published February 26, 2025
| Version v1
Dataset
Open
Harp: Platform Independent Deconvolution Tool
Authors/Creators
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1.
University of Regensburg
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2.
Leibniz Institute for Immunotherapy
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3.
University Hospital Regensburg
Contributors
Project leader:
Researchers:
Supervisor:
-
1.
University of Regensburg
- 2. Leibniz Institut für Immuntherapie (LIT)
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3.
University Hospital Regensburg
Description
Harp is a tool that estimates reference profiles and cell compositions for deconvolution of bulk transcriptomic data.
For evaluation the performance of Harp against other deconvolution tools we employed real bulk expression data (RNA-seq and microarray), along with their corresponding cell compositions from flow cytometry experiment as well as cell expression profiles measured through sorted RNA-seq and microarray technology.
These datasets contain combined processed RNA-seq, flow cytometry and microarray expression data that were utilized in the Harplication package, which applies the Harp algorithm along other deconvolution tools.
The original datasets are derived from the following studies:
- Bulk RNA-seq expression with paired flow cytometry from Zimmermann et al., 2016. The datasets were received via SDY67.
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Sorted RNA-seq expression data from Monaco et al., 2019 , available on NCBI under GEO accession number GSE107011.
- Microarray gene expression data from Newman et al., 2015, available on NCBI under GEO accession number GSE65133.
- Flow cytometry data from Newman et al., 2015, was received from the analysis of Vallania et al., 2018, also available on GSE65133.
- Microarray based reference from Newman et al., 2015, available on CIBERSORTx.
This project has received funding from
- The European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 860003.
- Bundesministerium für Bildung und Forschung (BMBF, German Federal Ministry of Education and Research) [031L0173].
Files
CIBERSORT_bulk_counts_gse65133_unnomalized_mapped.txt
Additional details
Dates
- Available
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2025-02-26
Software
- Repository URL
- https://github.com/spang-lab/harp
- Programming language
- R
- Development Status
- Active