ArticleJournal of statistical software2011
Using the R Package crlmm for Genotyping and Copy Number Estimation.
Article in Journal of statistical software, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
48 citing papers in PubMed.
- Relapsed diffuse large B-cell lymphoma present different genomic profiles between early and late relapses.Oncotarget · 2016Trial
- Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci.Human molecular genetics · 2016Trial
- Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies.bioRxiv : the preprint server for biology · 2026Article
- Investigating the mechanisms underlying resistance to chemoterapy and to CRISPR-Cas9 in cancer cell lines.Scientific reports · 2024Article
- Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes.Nature neuroscience · 2022Article
- COLONOMICS - integrative omics data of one hundred paired normal-tumoral samples from colon cancer patients.Scientific data · 2022Article
- Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR.Epigenetics & chromatin · 2021Article
- Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue.Clinical epigenetics · 2021Article
- Recent ultra-rare inherited variants implicate new autism candidate risk genes.Nature genetics · 2021Article
- DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment.Computational and structural biotechnology journal · 2021Article
- Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth.Science advances · 2020Article
- Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program.Stem cell research · 2020Article
- The Brazilian Initiative on Precision Medicine (BIPMed): fostering genomic data-sharing of underrepresented populations.NPJ genomic medicine · 2020Article
- Distribution of local ancestry and evidence of adaptation in admixed populations.Scientific reports · 2019Article
- Dysregulated protocadherin-pathway activity as an intrinsic defect in induced pluripotent stem cell-derived cortical interneurons from subjects with schizophrenia.Nature neuroscience · 2019Article
- Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes.NPJ genomic medicine · 2019Article
- A genome wide SNP genotyping study in the Tunisian population: specific reporting on a subset of common breast cancer risk loci.BMC cancer · 2018Article
- Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.Nature neuroscience · 2018Article
- HLA typing using genome wide data reveals susceptibility types for infections in a psychiatric disease enriched sample.Brain, behavior, and immunity · 2018Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Genotyping platforms such as Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations at millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools to assess copy number changes are more variable and often discordant. One explanation for the discordance is that copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. Analysis algorithms that do not adjust for batch effects are prone to spurious measures of association. The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number. This paper illustrates a workflow for the estimation of allele-specific copy number and integration of the marker-level estimates with complimentary Bioconductor software for inferring regions of copy number gain or loss. All analyses are performed in the statistical environment R.
Identifiers
22523482PMC3329223What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.