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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
We have developed a Bioconductor software package for examining differential expression of replicated count-based expression data. Expand
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
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
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. Expand
limma: Linear Models for Microarray Data
- G. Smyth
- Computer Science
A survey is given of differential expression analyses using the linear modeling features of the limma package. Expand
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-wide… Expand
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 a… Expand
Normalization of cDNA microarray data.
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
ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays.
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 provide… Expand
Moderated statistical tests for assessing differences in tag abundance
MOTIVATION Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. Expand
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 various… Expand