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awesome-multi-omics

A community-maintained list of software packages for multi-omics data analysis.

While many of the packages here are marketed for "omics" data (transcriptomics, proteomics, etc.), other more general terms for this type of data analysis are:

The common thread among the methods listed here is that the same samples are measured across different assays. The data can be described as multiple matrices/tables with the same number of samples and varying number of features.

The repo is in the style of Sean Davis' awesome-single-cell repo for single-cell analysis methods.

Contributions welcome...

For brevity, below lists only the first author of multi-omics methods.

Software packages and methods

Multi-omics correlation or factor analysis

Ecology multi-table literature

Chemometrics multi-table literature

Behavioral research multi-table literature

Multi-omics clustering / classification / prediction

Note: I think that prediction of genomic tracks, e.g. ChIP-seq, from other genomic tracks is a large area of research that may deserve a separate repository. Below are methods for clustering / classification of samples into sub-types or prediction of outcomes.

Multi-omics autoencoders

Multi-omics networks

Single cell multi-omics

Multi-study correlation or factor analysis

Multi-omics simulation

Multi-omics reviews / evaluations

Multi-omics application papers

Multi-omics data management

Batch effect correction

Meetings and workshops