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jingwyang / AnceTran

AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data

https://github.com/jingwyang/AnceTran

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more docs #2

Open antonkulaga opened 5 years ago

antonkulaga commented 5 years ago

Not clear from the README what is the core difference from TreeExp, support of Chip-Seq data? I am currently doing multi-species comparisons of gene expressions and I want to understand what are the optimal packages

jingwyang commented 5 years ago

hi @antonkulaga , AnceTran was developed only for the method of ancestral inference based on either RNA-seq or ChIP-seq data. And TreeExp is for expression data only and has integrated the methods including

pairwise expression distance estimation
relative rate test for transcriptome evolution
the strength of expression conservation estimation
ancestral transcriptome inference

So I recommend TreeExp for your analysis, and your can read the [Tutorial] (https://jingwyang.github.io/TreeExp-Tutorial/) for reference.