ascend clustering

Ascend clustering method from https://academic.oup.com/gigascience/article/8/8/giz087/5554286

Problem with newest version fom https://github.com/powellgenomicslab/ascend:

runPCA doesn't work, even on their own example dataset: unable to find an inherited method for function ‘int_colData’ for signature ‘"NULL"’

So falling back to the V0.5 used in Duo et al. clustering ("IMB-Computational-Genomics-Lab/ascend", ref = "b415c0918f10306829b64bfad37f5d08da049ef7").

Method template

This template will help you to add a method to an omnibenchmark project. For each method that you have, one dedicated repository has to be created from this template to upload the method on the renku system.

The configuration of a method module is explained in details in the Omnibenchmark documentation

To configure the project, please modify:

• src/ascend-clustering.py (if working with python) or src/ascend-clustering.R (if working with R) with your wrapper of a method to benchmark

• src/config.yaml, to configure the project and the dataset.

• requirements.txt or install.R if you need packages or modules installed.

You can check the requirements for this module by running:

import omniValidator as ov
ov.display_requirements(
    benchmark = "omni_clustering", # <-- the name of this Omnibenchmark
    keyword="omni_clustering_method" # <-- the keyword of this module
)

To run the project, then run

python ~/src/run_workflow.py

Once your module is completed and tested, you can integrate it in your Omnibenchmark by submitting it (open an issue) on the corresponding orchestrator page of your benchmark (link to the existing orchestrators).