Anthony Gitter
Anthony Gitter
Following up from #33, in this issue we can discuss how to edit the vignette to provide guidance about which genes to retain for clustering and which genes to remove...
Logging an idea that came up in the Discord discussion. https://chemicalsafety.com/sds-search/ provides access individually. [Chemical vendors](https://ors.od.nih.gov/sr/dohs/safety/laboratory/BioSafety/Pages/material_safety_data_main.aspx) also provide access to individual sheets. I did not yet find an open, bulk...
Related work that could be cited to show interest in using large language models for scientific writing assistance: The Role of AI in Drug Discovery: Challenges, Opportunities, and Strategies https://arxiv.org/abs/2212.08104...
I started looking through the code and was slowed down because some files import other modules that no longer exist. For example `model_LatentDiffusionDecoder.py` has ```python from ProteinDT.models.model_SDE import VESDE, VPSDE...
I found the current installation process challenging because it combines many calls to conda and pip. I simplified it by creating a conda .yml file to install almost all of...
What is your recommended citation for this package if it is referenced in a manuscript? Should we refer directly to the GitHub repository?
Requiring `sklearn` in `setup.py` installs the wrong package. The other changes make `requirements.txt` more consistent with `setup.py`. I found it tricky to install this package from `requirements.txt` and created a...
Calling `get_networkx_graph_as_dataframe_of_edges` on the augmented forest generated a data frame that has node names only for the edges that are in the optimal forest solution. For instance: ``` protein1 protein2...
When testing with a toy example, I received an error related to how `pcst_fast` is called: ``` Traceback (most recent call last): File "/miniconda3/envs/oi2/bin/OmicsIntegrator", line 8, in sys.exit(main()) File "/miniconda3/envs/oi2/lib/python3.6/site-packages/OmicsIntegrator/__main__.py",...
Numeric arguments, such as `g`, have `nargs='*'`, which stores them as a list: https://github.com/fraenkel-lab/OmicsIntegrator2/blob/ea1092fe0053556338cf29c4840a1ff35e8a4f81/src/__main__.py#L43-L44 That causes the parameter checks in `graph.py` to fail because they are not numeric: https://github.com/fraenkel-lab/OmicsIntegrator2/blob/ea1092fe0053556338cf29c4840a1ff35e8a4f81/src/graph.py#L144 Was...