Omics · study · 2026
Systematic Benchmarking of Ambient RNA decontamination Tools to Advance Precision in Single-Cell transcriptomic analysis
Listed in NCBI GEO
Ambient RNA contamination in single-cell RNA sequencing introduces exogenous transcripts from lysed cells, distorting cell-type annotation and biological interpretation.
Description
We performed a systematic benchmark of 7 decontamination tools using datasets with well-defined ground truth. Our evaluation across accuracy, robustness, and subtype sensitivity reveals complementary strengths: CellBender and scCDC excel in contamination estimation accuracy, SoupX is the most robust and sensitive for rare subtypes.
For overall decontamination efficacy, scAR best balanced robustness and accuracy at the cell-type level. Our study offers a practical guideline for context-dependent tool selection and highlights key directions for future algorithmic development.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE337nnn/GSE337237 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE337237 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1490887 ncbi.nlm.nih.gov/bioproject/PRJNA1490887 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Genome binding/occupancy profiling by high throughput sequencing · Mus musculus
- From keywords
- Life Sciences
- Inferred from text
- Bioinformatics and computational biology 71% · RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 75%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE337237 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].anzsrc:group:3102 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (71%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[method].geo_series_type:genome-binding-occupancy-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:10090 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |