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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
TLDR
We have developed a Bioconductor software package for examining differential expression of replicated count-based expression data. Expand
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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
  • G. Smyth
  • Computer Science, Medicine
  • Statistical applications in genetics and…
  • 12 February 2004
TLDR
We develop the hierarchical model of Lonnstedt and Speed (2002) into a practical approach for general microarray experiments with arbitrary numbers of treatments and RNA samples. Expand
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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
TLDR
We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. Expand
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limma: Linear Models for Microarray Data
TLDR
A survey is given of differential expression analyses using the linear modeling features of the limma package. Expand
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Gene ontology analysis for RNA-seq: accounting for selection bias
We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wideExpand
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voom: precision weights unlock linear model analysis tools for RNA-seq read counts
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates aExpand
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Normalization of cDNA microarray data.
TLDR
Normalization means to adjust microarray data for effects which arise from variation in the technology rather than from biological differences between the RNA samples or between printed probes. Expand
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ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays.
  • Yifang Hu, G. Smyth
  • Mathematics, Medicine
  • Journal of immunological methods
  • 15 August 2009
ELDA is a software application for limiting dilution analysis (LDA), with particular attention to the needs of stem cell assays. It is the first limiting dilution analysis software to provideExpand
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Moderated statistical tests for assessing differences in tag abundance
TLDR
MOTIVATION Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. Expand
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Small-sample estimation of negative binomial dispersion, with applications to SAGE data.
We derive a quantile-adjusted conditional maximum likelihood estimator for the dispersion parameter of the negative binomial distribution and compare its performance, in terms of bias, to variousExpand
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