Overview of new implementations about immunedeconv HOT 7 CLOSED

Two more things we need to think of:

• Could you please check the licenses of the methods, similar to this table? We need to be careful when including GPL-licensed code directly in the package and we'll need to update that table anyway.

• We'll need to take care of the dependency management. The package has already (too) many dependencies, and I'm a bit wary including more. Maybe the new packages should become optional dependencies, as Konstantin implemented it for omnideconv. Also all dependencies must be available on bioconda. If they are not, we'll need to add them. Could you maybe list the links to all packages and check which methods are already available from bioconda?

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In terms of External Dependencies we need to add:

• mMCP counter
• ComICS
• ConsensusTME
  None of this packages seems to be available on Bioconda. All the other methods will be added with their source code

Licenses

• mMCPcounter: GP-3.0

• seqImmuCC (requires CIBERSORT): CIBERSORT is free for non commercial use, and I am waiting for the authors to confirm the license for the rest

• DCQ (ComICS package): GPL-2.0

• BASE: not specified (source code is attached to the published paper)

• ABIS: GPL-2.0

• ConsensusTME: GPL-3.0

Datasets
Some datasets should be included in the package as well.

• mouse RNAseq + flow cytometry/FACS data. Just a few samples
• Human PBMC datasets (cf Francesca)
• Human cancer datasets (cf Francesca)

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Update from the authors: for the BASE algorithm there is no license so we can use it how we want

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Did they say that we can use it specifically? As I understand it, no license means technically you can not use it at all.

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@mlist "There is no license for BASE. Feel free to incorporate into your package." This is what they said.
They probably meant that there was no particular restriction

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Ok then :)

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@LorenzoMerotto, I thin you addressed all of this in #81?
Feel free to close the issue!

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