Hi!
I have 5 time points for mice development and I have miRNA and mRNA expression data (RNA-seq) for each time point. I would like to integrate these expression profiles in a dynamic way. I know the algorithm called mirDREM (http://www.sb.cs.cmu.edu/drem/mirdrem/) based on Input-Output Hidden Markov Models. Do you know other tools/algorithms?
I agree with Matthew - using a count based model like edgeR, DESeq are the way to go - down that ally you might also consider Kallisto + Sleuth.
Another cool thing to do would be to use the miRNA target databases to link miRNA and mRNA expression (databases such as miRTarBase (experimentally verified), or eimmo (integration of several sources of predicted targets).
I agree with Matthew - using a count based model like edgeR, DESeq are the way to go - down that ally you might also consider Kallisto + Sleuth.
Another cool thing to do would be to use the miRNA target databases to link miRNA and mRNA expression (databases such as miRTarBase (experimentally verified), or eimmo (integration of several sources of predicted targets).
See my papers about Matroska feature selection for microarray data from RG.
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- Biological Science
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