Dear all,
I just wondering if there is any packages for differential expression analysis of Time course RNAseq counts data? I used Next msSigPro but I would like to compare results of this with some other packages.
Thank you
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written
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bioinforupesh2009.au •
Please see the many similar posts to the right ----------->
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Devon Ryan
Thank you Devon for your kind reply.....I know that edgeR and DESEq2 are also dealing with time series but I would like to have similar packages like maSigPro as this packages shows profiling of each differential expressed gene across all the all time points.
Are plots here what you are interested in: http://www.bioconductor.org/help/workflows/rnaseqGene/#time
Note that such plots can be made for the significant genes from any package (DESeq, edgeR, etc). For that plot I added a simple loess line to the plot of normalized counts to help visually connect the groups, but I might add a function to give the actual fitted normalized counts from the model, which are t(t(assays(dds)[["mu"]])/sizeFactors(dds))
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Michael Love
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