genome-maps - An open-source high-performance web-based HTML5 genome browser. Genome Maps can be customized and allow browsing user data such as BAM and VCF files among other formats.
Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: Release (3.8)
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Author: Michael Love, Simon Anders, Wolfgang Huber
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
Citation (from within R, enter citation("DESeq2")):
Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8.
This protocol provides detailed instructions on Quality Control, EWAS, and CpG island signature discovery with Illumina Infinitum MethylationEPIC and Infinium Human Methylation 450K BeadChip data. R package minfi and caret was used in this analysis.