mikelove / awesome-multi-omics Goto Github PK

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

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

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?

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

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?