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Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

Cell Reports Methods(2022)10.1016/j.crmeth.2022.100321Source: DataRank Database

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects is a research paper published in Cell Reports Methods (2022). On theSindex it has a DataRank of 0.737. It has been cited 20 times, with 20 citing works in its 1-hop citation network.

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0.737DataRank · unranked

Scored on demand from live citation data

Deposits data Open Access20 citations · 20 citing works in its network

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Data availability

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

figshare10.6084/m9.figshare.c.4436264.v1

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›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (3 grants)OA: goldTopics (29)IDs (PubMed)

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 62%Citation Network 38%

Base Score Contribution

0.457

From this paper's citation signal

Citation Network Contribution

0.280

From 14 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 20 citers.

Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?
bioRxiv (Cold Spring Harbor Laboratory)20243 citations34 referencesContributes 0.041
A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information
Genome biology20255 citations45 referencesContributes 0.040
On the identification of differentially-active transcription factors from ATAC-seq data
PLoS Computational Biology20245 citations46 referencesContributes 0.039
Context transcription factors establish cooperative environments and mediate enhancer communication
Nature Genetics202417 citations78 referencesContributes 0.037
Activity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders
Biological Psychiatry202317 citations80 referencesContributes 0.036

Authors (7)

Hsin-Jung Chou ORCID,Hector Roux de Bézieux ORCID,Kelly Street ORCID,Davide Risso ORCID,John Ngai ORCID

Live enrichment

PubMed:19910364

Fonds Wetenschappelijk Onderzoek

Grant: 1246220N

National Institutes of Health

Grant: R01 DC007235

National Institutes of Health

Grant: 5R01DC007235-13

Programs of Gene Expression in Olfactory Neurogenesis

goldLicense: cc-by-nc-nd

publisherhttps://ars.els-cdn.com/content/image/1-s2.0-S2667237522002119-fx1_lrg.jpg

publisherhttps://api.elsevier.com/content/article/PII:S2667237522002119?httpAccept=text/xml

publisherhttps://api.elsevier.com/content/article/PII:S2667237522002119?httpAccept=text/plain

repositoryhttp://hdl.handle.net/1854/LU-01HW2H7J238EQPWZ8MV7RESX6A

repositoryhttps://escholarship.org/uc/item/3ms781g2

Fields of Study

0301 basic medicine03 medical and health sciences0303 health sciences

Keywords

570GENESBioinformatics and Computational BiologyREDUCES SYSTEMATIC-ERRORSBIOCONDUCTOR PACKAGEArticleEpigenesis, GeneticREPRODUCIBILITYGeneticsdifferential accessibilityGC-contentLANDSCAPEepigeneticsHuman Genome500Biology and Life SciencesCHIP-SEQHigh-Throughput Nucleotide SequencingATAC-seqSequence Analysis, DNABiological SciencesOPEN CHROMATINnormalizationBIASChromatin Immunoprecipitation Sequencingclustering