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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TLDR
This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Differential expression analysis for sequence count data
TLDR
A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.
HTSeq—a Python framework to work with high-throughput sequencing data
TLDR
This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis, and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
Differential expression analysis for sequence count data
TLDR
An error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data is proposed and provides good detection power.
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TLDR
This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Orchestrating high-throughput genomic analysis with Bioconductor
TLDR
An overview of Bioconductor, an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology, which comprises 934 interoperable packages contributed by a large, diverse community of scientists.
Software for Computing and Annotating Genomic Ranges
TLDR
This work describes Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions, including those for sequence analysis, differential expression analysis and visualization.
Detecting differential usage of exons from RNA-seq data.
TLDR
DEXSeq is presented, a statistical method to test for differential exon usage in RNA-seq data that uses generalized linear models and offers reliable control of false discoveries by taking biological variation into account.
Bidirectional promoters generate pervasive transcription in yeast
TLDR
It is shown that both SUTs and CUTs display distinct patterns of distribution at specific locations, changing the view of how a genome is transcribed and indicating that bidirectionality is an inherent feature of promoters.
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