Add a method

[rcannood]

• Install dependencies
• Clone the repository with

  git clone --recursive git@github.com:openproblems-bio/task_cyto_batch_integration.git

• Sync resources with:

  scripts/sync_resources.sh

• Create a new branch (e.g. add-<name of method>)
• Create a method by filling a name in scripts/create_component/create_r_method.sh or scripts/create_component/create_python_method.sh and running the script
• Edit the src/methods/<name of method> files to implement your component

[rcannood]

@rcannood @SofieVG @ghar1821 @KatrienQ @LuLeom

Can you mention which method you're adding so we can avoid duplicating our efforts?

First come, first served!

[ghar1821]

I'm going to finish off harmonypy then start on cycombine

[LuLeom]

Will start with CytoNorm(py), then BatchAdjust

[rcannood]

I'll take a look at limma removeBatchEffect!

[rcannood]

Harmonypy and limma removeBatchEffect have been merged.

@LuLeom Any progress on CytoNorm and BatchAdjust?

@ghar1821 What about cycombine?

[LuLeom]

@LuLeom Any progress on CytoNorm and BatchAdjust?

CytoNormpy is still in the beta and does not work for the time being. We might switch to the R version.
I am planning to finalise batchadjust by next week.

Combat has also been implemented (PR #25 )