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Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries

Genome Research(2024)10.1101/gr.277066.122Source: DataRank Database

Benchmarking bulk and single-cell variant-calling approaches on Chromium scRNA-seq and scATAC-seq libraries is a research paper published in Genome Research (2024). On theSindex it has a DataRank of 0.306. It has been cited 6 times, with 6 citing works in its 1-hop citation network.

N/A

0.306DataRank · unranked

Scored on demand from live citation data

Deposits data Open Access6 citations · 6 citing works in its network

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Linked data & code

geo bioproject doi

Data availability

Repositories this paper deposited data in (declared in PubMed).

GEOGSE213338 GSE213503
BioProjectPRJNA1099909

DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?

›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (6 grants)OA: bronzeTopics (40)IDs (PubMed, PMC, OpenAlex)Annotations (3)

FAIR Checklist

Context only (not used in score)

Findable (1/2)

Has DOI

Accessible (1/2)

Open Access

Interoperable (0/2)

Reusable (0/3)

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DataRank Breakdown

Base Score 95%Citation Network 5%

Base Score Contribution

0.292

From this paper's citation signal

Citation Network Contribution

0.0143

From 1 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 6 citers.

Identification of malignant cells in single-cell transcriptomics data
Communications Biology20259 citations137 referencesContributes 0.017
VAETracer: Mutation-Guided Lineage Reconstruction and Generational State Inference from scRNA-seq
bioRxiv (Cold Spring Harbor Laboratory)20260 citations52 referencesContributes 0.000
A network-based deep learning model integrating subclonal architecture for therapy response prediction in cancer
bioRxiv (Cold Spring Harbor Laboratory)20260 citations68 referencesContributes 0.000
Hidden in the Noise: Low-Variant Allele Frequency Mutations and Their Impact on Precision Oncology
Journal of Genome Biotechnology and Genetics20260 citations120 referencesContributes 0.000
A network-based deep learning model integrating subclonal architecture for therapy response prediction in cancer
Cell Reports Methods20260 citations60 referencesContributes 0.000

Authors (5)

Hossein Farahani ORCID,R. Wilder Scott ORCID,T. Michael Underhill ORCID,Ali Bashashati ORCID,Matthew V. J. Wiens ORCID

Live enrichment

PubMed:39147582 PMC:PMC11444184 OpenAlex:https://openalex.org/W4401607313

Terry Fox New Frontiers

Grant: 1021

National Institutes of Health

Grant: CA231652

Natural Sciences and Engineering Research Council of Canada

Grant: RGPIN-2019-04896

NCI NIH HHS

Grant: U54 CA231652

Natural Sciences and Engineering Research Council of Canada

Grant: unidentified

unidentified

National Institutes of Health

Grant: 1U54CA231652-01

Targeting SS18-SSX biology in synovial sarcomagenesis

bronzeLicense: cc-by-nc

journalhttps://genome.cshlp.org/content/early/2024/08/15/gr.277066.122.full.pdf

publisherhttps://genome.cshlp.org/content/early/2024/08/15/gr.277066.122.full.pdf

publisherhttps://syndication.highwire.org/content/doi/10.1101/gr.277066.122

journalhttps://doi.org/10.1101/gr.277066.122

repositoryhttps://pubmed.ncbi.nlm.nih.gov/39147582

Fields of Study

Single-cell and spatial transcriptomicsCancer Genomics and DiagnosticsCRISPR and Genetic Engineering0301 basic medicine0303 health sciences03 medical and health sciencesSingle-Cell AnalysisHumansChromiumBenchmarkingGene LibrarySequence Analysis, RNARNA-SeqHigh-Throughput Nucleotide SequencingGenetic VariationSingle-Cell Gene Expression Analysis

MeSH Terms

RNA-SeqSingle-Cell Gene Expression AnalysisChromiumHumansGenetic VariationGene LibrarySequence Analysis, RNABenchmarkingSingle-Cell AnalysisHigh-Throughput Nucleotide Sequencing

Keywords

BiologyComputational biologyBenchmarkingGeneticsChromiumSequence Analysis, RNAHigh-Throughput Nucleotide SequencingGenetic VariationSingle-Cell Gene Expression AnalysisMethodsHumansRNA-SeqSingle-Cell AnalysisGene Library