SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Bioinform.

• Publication date

  2011-01-15

• Fields of study

  Biology, Medicine, Computer Science, Mathematics

• Identifiers
  DOI 10.1093/bioinformatics/btq650PMID 21098430
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2010influential reference
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