mikelove / awesome-multi-omics Goto Github PK

Hello, would you please consider adding D-CCA on your list of "Multi-omics correlation or factor analysis"?
Link: https://github.com/shu-hai/D-CCA
Paper: https://doi.org/10.1080/01621459.2018.1543599

Thanks.

I was thinking about adding Integrative pathway enrichment analysis of multivariate omics data by Paczkowska et al from the recent PCAWG release.

2020 - Paczkowska - Integrative pathway enrichment analysis of multivariate omics data

But I am not sure where to put it - there is no obvious category for it. Any suggestions?

In the review "Multi-omics Data Integration, Interpretation, and Its Application", which is already listed here, there are some mentions of methods not listed here.

I open the issue in case I forget to add them later, but perhaps they are not included because they are the ones in FUSION and are not multi-table (Although I need to explore them): PFA, SNF and PSDF

Hi Mike,
Is it worth adding a brief description to each of the types of multi-omics data at the top of the README for students / newcomers? For example,

• Multi-modal (brief description of multi-modal data here, such as "data in multiple different structures but that share samples, such as brain imaging and metabolomics data recorded on the same subjects")
• Multi-table (brief description of multi-table data here, such as "data in the same structure and shared feature space across different cohorts [different batch effects], such as transcriptomics analysis of multiple independent cohorts of patients with the same cancer")
• Multi-way (brief description of multi-way data here, such as "data in multiple tables which share both samples and features, often represented as a 3-dimensional array or tensor, such as single -omics data recorded on the same cohort regularly over multiple time points or across tissue samples")

What do you think?

There are some tools that can be used to simulate multi-omics dataset. Maybe a new category could be added?

Here are a few I know:

• 2016 - InterSIM - Chalise - methylation, gene expression and protein expression - paper
• 2019 - MOSim - Martinez-Mira - RNA-seq, ATAC-seq (DNase-seq), ChIP-seq, small RNA-seq and Methyl-seq. - preprint
• 2019 - OmicsSIMLA - Chung - - paper

Not sure it fits the repository conditions, as the software is not for multi-tables but multi-networks.

• 2020 - MOGAMUN A multi-objective genetic algorithm to find active modules in multiplex biological networks preprint