R: A Language for Data Analysis and Graphics

Ihaka, Ross; Gentleman, Robert

doi:10.2307/1390807

Cited by 5,242 publications

(4,122 citation statements)

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“…To determine whether there were any consistent differences between genome regions in SNP abundance, the distribution and identity of SNP were analysed in 1-Mb non-overlapping bins and the results plotted using the R project software (Ihaka and Gentleman 1996) downloaded from http://www.r-project. org/, verified 1 December 2011.…”

Section: Methodsmentioning

confidence: 99%

Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms

et al. 2012

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Abstract. We sequenced the genomes of a Brahman, an Africander and a Tuli bull because tropically adapted breeds of cattle have so far not been well characterised at the level of DNA variation. In excess of 16 Gb of Illumina GA-II sequence was obtained for each animal in the form of 75-bp paired-end reads, generating more than 6· coverage of each genome, and between 86.7 and 88.8% of the bases of each genome sequence was covered by one or more sequence reads. A total of 6.35 million single nucleotide polymorphisms (SNP) were discovered in the three animals, adding 3.56 million new SNP to dbSNP. The Brahman animal had nearly twice as many SNP as either the Tuli or the Africander. Comparing genome sequence to genotypic array data, genotype accuracy from sequencing was more than 98% for homozygotes that had at least six high quality sequence reads and for heterozygotes that had at least two high quality reads containing the alternative allele. Intergenic and intronic SNP were found at higher densities closer to coding sequences, and there was a reduction in numbers of SNP within 5 bp of a splice site, features consistent with genetic selection. On average, slightly more SNP per Mb, and slightly higher average reads per SNP per Mb, were found towards the ends of chromosomes, especially towards the telomeric end of the chromosome. At least one autosome in each animal showed a large stretch of homozygosity, the largest was 58 Mb long in the Tuli, although the animals are not known to have recent inbreeding.

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Section: Methodsmentioning

confidence: 99%

Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms

et al. 2012

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“…10 Association between WHOQOL-BREF physical, psychological, social relationships and environmental domain scores and hospital stay, age, sex and ISS variables were analyzed with linear regression models. When these models are adjusted, the coeffi cient of determination (R 2 ) provides an estimate of proportion of each domain's variability, explained by the group of variables analyzed.…”

Section: Methodsmentioning

confidence: 99%

Qualidade de vida de vítimas de trauma seis meses após a alta hospitalar

Alves

Salim

Martinez³

et al. 2009

Rev. Saúde Pública

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OBJETIVO: O trauma ocupa o terceiro lugar dentre as causas de morte no Brasil. Contudo, seu impacto na qualidade de vida dos sobreviventes tem sido pouco estudado no País. O objetivo do estudo foi avaliar a qualidade de vida de vítimas de trauma atendidas em unidade hospitalar de emergências, seis meses após a alta hospitalar. MÉTODOS: Foram incluídos 35 pacientes de unidade de emergência de hospital universitário de Ribeirão Preto (SP), entre 2005 e 2006. Os pacientes foram entrevistados em seus domicílios, seis meses após terem tido alta hospitalar. Foi aplicado o instrumento World Health Organization Quality of Life, versão breve, para avaliação dos domínios físico, psicológico, relações sociais e meio ambiente. As associações entre os escores dos domínios e as variáveis permanência hospitalar, idade, sexo e Injury Severity Score foram exploradas por modelos de regressão linear. RESULTADOS: Observou-se diminuição significativa na qualidade de vida do grupo estudado, quando comparado a amostras de pessoas normais em estudos nacionais e internacionais, em particular nos domínios físico, psicológico e de meio ambiente. O domínio relações sociais apresentou a maior média de escores, com 69,7 pontos, enquanto o domínio meio ambiente recebeu a menor pontuação (52,4), ambos na escala percentual. As variáveis associadas a domínio físico foram permanência hospitalar (p=0,02), idade (p<0,01) e sexo (p=0,03). Para os demais domínios, a análise não mostrou associação com as variáveis estudadas. CONCLUSÕES: As vítimas de trauma apresentaram diminuição nos escores de qualidade de vida. Embora o aspecto físico tenha sido o mais atingido, há evidências de que os domínios psicológico e de meio ambiente permaneceram distantes das condições ideais esperadas para a população em geral.

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“…(2017) study of Le Conte's thrashers ( Toxostoma lecontei ) in estimating negligible migration among subspecies to recommend conservation status across their Western North American range. Other tools to test complex demographic models using genomic data include coalescent simulation‐based methods (e.g., FASTSIMCOAL; Excoffier & Foll, 2011; Excoffier, Dupanloup, Huerta‐Sánchez, Sousa, & Foll, 2013), Approximate Bayesian Computation (ABC; Beaumont, Zhang, & Balding, 2002; Robinson, Bunnefeld, Hearn, Stone, & Hickerson, 2014)‐based methods that compare summary statistic distributions in simulated versus observed populations, and diffusion approximations to the joint allele frequency spectrum for demographic inference (e.g., ∂ a ∂ i , Gutenkunst, Hernandez, Williamson, & Bustamante, 2009). In general, model‐based estimation of evolutionary demographic history (both ancient and recent) when applied in combination with summary population genetic statistics as described above (including F ST , inbreeding coefficients, and homozygosity), and non‐model‐based methods (including STRUCTURE and ADMIXTURE; Alexander, Novembre, & Lange, 2009; Pritchard et al., 2000) can prove to be useful means to bridge genomics and conservation in particular.…”

Section: Improving Downstream Computational Analysesmentioning

confidence: 99%

Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.

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R: A Language for Data Analysis and Graphics

Cited by 5,242 publications

References 0 publications

Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms

Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms

Qualidade de vida de vítimas de trauma seis meses após a alta hospitalar

Recent advances in conservation and population genomics data analysis

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