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Orchestrating high-throughput genomic analysis with Bioconductor
Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology with 934 interoperable packages contributed by a large, diverse community of scientists. Expand
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Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
We compare statistical methods for detecting genes that are significantly DE between two types of biological samples and find that there are substantial differences in how the test statistics handle low-count genes. Expand
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Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
MOTIVATION The recently released Infinium HumanMethylation450 array (the '450k' array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci across a range of genomic features. Expand
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BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
DNA methylation is an important epigenetic modification involved in gene regulation, which can now be measured using whole-genome bisulfite sequencing. However, cost, complexity of the data, and lackExpand
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Biases in Illumina transcriptome sequencing caused by random hexamer priming
Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias isExpand
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Increased methylation variation in epigenetic domains across cancer types
Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which alsoExpand
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Removing technical variability in RNA-seq data using conditional quantile normalization
The ability to measure gene expression on a genome-wide scale is one of the most promising accomplishments in molecular biology. Microarrays, the technology that first permitted this, were riddledExpand
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Reversible switching between epigenetic states in honeybee behavioral subcastes
In honeybee societies, distinct caste phenotypes are created from the same genotype, suggesting a role for epigenetics in deriving these behaviorally different phenotypes. We found no differences inExpand
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Conservation of an RNA regulatory map between Drosophila and mammals.
Alternative splicing is generally controlled by proteins that bind directly to regulatory sequence elements and either activate or repress splicing of adjacent splice sites in a target pre-mRNA.Expand
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Social environment is associated with gene regulatory variation in the rhesus macaque immune system
Variation in the social environment is a fundamental component of many vertebrate societies. In humans and other primates, adverse social environments often translate into lasting physiologicalExpand
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