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Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.07.570603Source: DataRank Database

Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues is a research paper published in bioRxiv (Cold Spring Harbor Laboratory) (2023). On theSindex it has a DataRank of 2.7. It has been cited 80 times, with 74 citing works in its 1-hop citation network.

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2.7DataRank · unranked

Scored on demand from live citation data

Open Access80 citations · 74 citing works in its network

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›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (5 grants)OA: greenTopics (24)Linked Datasets (8)DataCite Reuse (8)IDs (PubMed, OpenAlex)

FAIR Checklist

Context only (not used in score)

Findable (2/2)

Has DOI
Indexed in repositories

Accessible (1/2)

Open Access

Interoperable (2/2)

DataCite relations
Linked datasets

Reusable (0/3)

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DataRank Breakdown

Base Score 24%Citation Network 76%

Base Score Contribution

0.659

From this paper's citation signal

Citation Network Contribution

2.1

From 63 citing papers with measurable signal

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Top 5 citers driving the network score

Ranked by each citer's contribution to N(p) — log1p(C_q) divided by its reference count — out of 74 citers.

A practical guide for choosing an optimal spatial transcriptomics technology from seven major commercially available options
BMC Genomics202566 citations23 referencesContributes 0.183
A Comparative Analysis of Imaging-Based Spatial Transcriptomics Platforms
bioRxiv (Cold Spring Harbor Laboratory)202371 citations25 referencesContributes 0.171
Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples
Nature Communications202526 citations30 referencesContributes 0.110
Gene count normalization in single-cell imaging-based spatially resolved transcriptomics
Genome biology202424 citations41 referencesContributes 0.079
Comparative analysis of multiplexed in situ gene expression profiling technologies
bioRxiv (Cold Spring Harbor Laboratory)202433 citations46 referencesContributes 0.077

Authors (13)

Ruixu Huang ORCID,Jack Nelson,Ce Gao ORCID,Miles Tran ORCID,Anna H. Yeaton ORCID

Live enrichment

PubMed:38106230 OpenAlex:https://openalex.org/W4389498204

National Institutes of Health

Grant: 5K08AR077037-03

Pathogenic fibroblast differentiation in rheumatoid arthritis

National Institutes of Health

Grant: 3P20GM130454-05S2

NOSI cloud computing Supplement

NIAMS NIH HHS

Grant: K08 AR077037

NIGMS NIH HHS

Grant: P20 GM130454

NCI NIH HHS

Grant: U2C CA233195

greenLicense: cc-by-nc-nd

repositoryhttps://www.biorxiv.org/content/biorxiv/early/2023/12/19/2023.12.07.570603.full.pdf

publisherhttps://syndication.highwire.org/content/doi/10.1101/2023.12.07.570603

repositoryhttps://doi.org/10.1101/2023.12.07.570603

repositoryhttps://pubmed.ncbi.nlm.nih.gov/38106230

Fields of Study

Single-cell and spatial transcriptomicsMolecular Biology Techniques and ApplicationsGene expression and cancer classification0206 medical engineering02 engineering and technology

Keywords

BenchmarkingBenchmark (surveying)Computational biologyCluster analysisTranscriptomeDNA microarrayComputer scienceGeneBiologySegmentationPattern recognition (psychology)Data miningBioinformaticsArtificial intelligenceGene expressionGeneticsCartographyGeographyArticle

Additional file 1 of Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

10.6084/m9.figshare.26732935.v1figshare

Additional file 1 of Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

10.6084/m9.figshare.26732935figshare

Additional file 2 of Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

10.6084/m9.figshare.26732938.v1figshare

Additional file 2 of Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

10.6084/m9.figshare.26732938figshare

Additional file 4 of Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

10.6084/m9.figshare.26732944.v1figshare

Additional file 4 of Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

10.6084/m9.figshare.26732944figshare