Adding Tiger

[cchen22]

Add TIGER.R from https://github.com/cchen22/TIGER

[codecov]

Codecov Report

Patch coverage has no change and project coverage change: -2.55 ⚠️

Comparison is base (d1d4038) 53.86% compared to head (419c7ec) 51.31%.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #272      +/-   ##
==========================================
- Coverage   53.86%   51.31%   -2.55%     
==========================================
  Files          18       19       +1     
  Lines        2276     2389     +113     
==========================================
  Hits         1226     1226              
- Misses       1050     1163     +113     

Impacted Files	Coverage Δ
R/TIGER.R	0.00% <0.00%> (ø)

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[marouenbg]

Hey @cchen22 , thank you for this great contribution.
Can you please transform the readme.md from your repo https://github.com/cchen22/TIGER/blob/master/README.md to a Jupyter notebook and push it as a vignette in netbooks, you can create a PR here: https://github.com/netZoo/netbooks/tree/main/netbooks/netZooR

[cchen22]

Hey @cchen22 , thank you for this great contribution. Can you please transform the readme.md from your repo https://github.com/cchen22/TIGER/blob/master/README.md to a Jupyter notebook and push it as a vignette in netbooks, you can create a PR here: https://github.com/netZoo/netbooks/tree/main/netbooks/netZooR

Hi @marouenbg , pull request for the TIGER.ipynb notebook was created: netZoo/netbooks#11.
However, for the current pull request of the TIGER.R code, I am a little confused about the "codecov" coverage report issue. Do you have any suggestions?

[marouenbg]

This is great, thank you @cchen22 !
No problem at all with codecov, it is complaining because we did not provide a test for the function. I need to check a couple of things for the integration and I will get back to you!

[marouenbg]

Hi @cchen22 ,
Happy new year! I haven't forgotten about this, I waiting for an older PR to correct an old release, then we add TIGER in.

[cchen22]

Hi @marouenbg ,
Happy new year! Please take your time and let me know if there is any issue with TIGER.

[marouenbg]

Hey @cchen22 ,

Sorry this took so long, we had a Bioconductor issue that we just fixed.
So can you have a final quick look at this before merging into devel?

Also new method contributions have to verify a few points. We have moved to a new phase in netZoo and our goals are to i) increase novelty and diversity of methods, ii) expand to new algorithms and statistical paradigms, and iii) increase the impact of each individual method:

• Moving forward, we make a distinction between a 'method' and a 'use case application'. A new netZoo method has to:
  • have enough novelty in comparison to existing methods (Merely changing PANDA inputs as in PUMA/SPIDER no longer qualifies as a distinct method but rather as a use case of PANDA)
  • be general for more than one setting or one dataset/disease
  • use case applications are application of off-the-shelf frameworks (such as deep learning models) for a particular question in genomic and therefore do not warrant a new method description.
  • Pipelines of existing methods such as CONDOR does not qualify as a new method
  • Use cases are all other submissions that do not fall under the previous points and therefore are better suited as Jupyter Notebooks for a Netbooks submission
• Method code has to have a set of small, fast-running unit tests to be integrated within the continuous integration server.
• Once merged in netZoo, please use the netZoo implementation, which will help detect bugs and fix them. Also, this will ensure that updates from other users are included in the version you maintain.
• Remove any other distributions of the method such as in GitHub or conda/bioconductor. The goal of netZoo is to provide a single drop point for network method we use and avoid parallel development branches of the same method
• The new method is maintained through netZoo--Once merged in devel, please install netZooR devel and see if the method works as intended. Please maintain and update new versions through netZooR by using pull requests
• To enhance reproducibility, please mention netZooR v1.4 in your manuscript software availability statement
• Also, please mention the netZoo publication, the basic goal of the netZoo project is to concentrate the attention on netZoo methods as opposed to individual efforts, e.g., users interested in TIGER may know about PUMA through the netZoo website and vice-versa.
• You can also upload your method use case as a Jupyter notebook in Netbooks. Methods with vignettes and use cases tend to have a better traction within the community. Typically a vignette notebook explains the rationale, the underlying math/statistical approach, and the parameters, while a use case notebook runs the biological application and reproduces figures from the paper.

[marouenbg]

Feel free to reopen when you're ready to proceed!

[cchen22]

Hi @marouenbg

Apologies for the delayed response. I have been preoccupied with my graduation requirements this month. I am now ready to incorporate TIGER into netzooR, which I am really looking forward to.

I reviewed your checklist and it seems TIGER meets most of the criteria. I will delete my GitHub repository after merging TIGER into netzooR. I will also be sure to acknowledge netzooR in the TIGER manuscript.
Please let me know if there are any specific items I should double-check before merging.

Thank you,
Chen

[marouenbg]

Congrats @cchen22, this is great to hear ! 🥳
Let's resume netZooR integration then