Joe Wandy

Run pathway analysis

1

Pathway analysis using PALS can be run in: - Single-omics - Multi-omics

See https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html Seems like deseq can do it? https://www.biostars.org/p/317023/ Also see https://biofam.github.io/MOFA2/faq.html for MOFA @KeqingWangg

It would be nice to switch the underlying backend objects to MuData https://github.com/pmbio/mudata, as that would make this package interoperable with [Muon](https://github.com/PMBio/muon). We should investigate this.

And also some form of CI

Remote APIs

2

If we detect that Reactome/neo4j is not installed on localhost, it should be possible to submit a POST request of the data to be mapped to the WebOmics server (instead...

Run factor analysis

1

using e.g. MOFA https://biofam.github.io/MOFA2/

1. Separate test data out from this repo into its own 2. Add methods that can be used to easily download test data

1. A feature could be assigned multiple annotations (names). 2. Users should be able to select which annotations to use, e.g. KEGG, ChEBI for compound data. before running analysis. 3....

1. Add codes to remove missing data (above a certain threshold) 2. Add codes to imput missing data (KNN, or others) 3. Add codes to normalise data (log, quantile normalisation)

Add some common plots to explore the data: 1. volcano plot 2. boxplot 3. density plot 4. heatmap Could use plotly so it can be easily rendered on web pages...