External data for MOFA (Multi-Omics Factor Analysis)

This repository contains external data for the MOFA package, including data sets, gene sets for enrichment analysis and others.

Multi-omic data sets

We currently provide parsed data and tutorials for the following studies:

• A cohort of 200 chronic lymphocytic leukaemia patients: patients were profiled by RNA expression, DNA methylation, drug response and somatic mutations. This is the first data set analysed in the paper.

  data("CLL_data")

• Single-cell multi-omics profiling of ~100 mouse embryonic stem cells.: single cells were profiled for DNA methylation and RNA expression using scNMT-seq. This is the second data set analysed in the paper.

  data("scMT_data")

If you have done an analysis with MOFA that you are proud of, please share it with us and we will add in our vignettes.

Gene sets

We provide curated gene sets from the Reactome and the MSigDB data base for the runEnrichmentAnalysis function. Please read the file documentations (?reactomeGS) for details on the format.

• Reactome

data("reactomeGS")

• MSigDB

  data("MSigDB_v6.0_C2_mouse")
  data("MSigDB_v6.0_C5_mouse")
  data("MSigDB_v6.0_C2_human")
  data("MSigDB_v6.0_C5_human")

If you have an annotation that other people could benefit from, please let us know and we will upload it.

Contact

The package is maintained by Ricard Argelaguet (ricard@ebi.ac.uk) and Britta Velten (britta.velten@embl.de). Please, reach us for problems, comments or suggestions. You can also contact us via a Slack group where we provide quick (and personalised!) help, this is the link.