Using mixomics to integrate bulk HiC RNAseq and Chipseq

Analysis
1

Dear all

I am in a dilemma and search of a package/tool that I can use to integrate various bulk datasets. We have a control-knockout experiment for which we have Bulk RNAseq, ChipSeq, ATACSeq and Hi-C data. We are able to analyze it separately but we wish to integrate all 4 (even if 3 is possible will help). I was wondering if mixOmics can be used to integrate the data.

Note: This is not multimodal data. However, we harvested cells at same time points (both in Ctrl and knockout). Again ChipSeq and RNAseq aren’t from same cells, just that cells are harvested around same time point. I believe therefore that diagonal integration will be ideal.

We wish to identify regulatory modules and how TFs influence gene and how Chromosomal landscape changes post knockout as compared to control

2

The MINT framework (horizontal integration) won’t apply here as each block is of a different omics type. Regarding DIABLO (vertical integration), is it only the ChipSeq and RNAseq that aren’t from the same cells? If the other datasets were recorded on the same cells then multiblock analysis will be the way to go.

Assuming that the samples within each dataset are unique, you may be forced into pairwise sPLS analysis. I don’t believe mixOmics can aid in this integration if this is the case. I’ll have a think of potentially any other methods you could use.