MOFA was used to analyze RNA-seq data and ChIP-seq data for 3 histone marks together, looking for sources of variation shared acorss all data types. Two different analyses were done, one with ChIP-seq reads counted in promoter regions, and one with ChIP-seq reads counted in called peaks. Each analysis is split into two steps. The first step (“run”) is fitting the model (which takes a long time) and performing some basic QC, while the second step (“analyze”) loads the fitted model and performs some analysis.
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