wallet-maker / cytopus Goto Github PK

Hi there! Me again 😄

I was successful at created a curated KnowledgeBase for my data (think). I'm trying to use it with Spectra now but am unsure how to get the required gene_set_dictionary from the KnowledgeBase. Looking for the equivalent to annotations = spc.default_gene_sets.load()

Thank you!

Hi there!

Thank you so much for making the knowledge base! I'm so excited to use it.

I wanted to make use of this knowledge base, but my data is not solely focused on leukocytes/immune cells. I was looking for an "easy" way to browse all the datasets + cell types and be able to remove the cell types that aren't applicable, and add new gene sets that are applicable.

I saw the tutorial on how to make your own knowledge base, but I'm interested in adding and editing the Cytopus knowledge base.

Is this something that is possible? I was browsing files like this, but it seems like it's not in a human readable format.

Thanks for the help!

I'm trying to get epithelial cells processes, but I get the error below.

There is no error if I put B instead of epi, for instance.

I have installed cytopus from github master 2 days ago.

> cytopus_graph.get_celltype_processes(["epi"], global_celltypes=["all-cells"], get_parents=False)

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-73-001d32070ef2> in <module>
----> 1 cytopus_graph.get_celltype_processes(["epi"], global_celltypes=["all-cells"], get_parents=False)

/projects/b1038/Pulmonary/nmarkov/ssc-v2/code/spectra_env/lib/python3.9/site-packages/cytopus/KnowledgeBase/kb_queries.py in get_celltype_processes(self, celltypes, global_celltypes, get_parents, get_children, parent_depth, child_depth, fill_missing, parent_depth_dict, child_depth_dict)
    229             process_dict[key] = {}
    230             for gene_set in value:
--> 231                 process_dict[key][gene_set] = gene_set_dict[gene_set]
    232         if global_celltypes != None:
    233             global_gs = {}

KeyError: 'crc-carcinoma-cell_cilia_Ganesh-mod1'

hello,

I am trying to use cytopus (in order to use Spectra) but I am running with issues since trying to import the module.I am currently working on an EC2 instance, Ubuntu 22.04.1 LTS (GNU/Linux 6.2.0-1012-aws x86_64)

I ran:

import cytopus as cp

but I got the following error:

ITraceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/ubuntu/anaconda3/envs/scFates-gpu/lib/python3.8/site-packages/cytopus/__init__.py", line 3, in <module>
    from . import KnowledgeBase as kb
ImportError: cannot import name 'KnowledgeBase' from partially initialized module 'cytopus' (most likely due to a circular import) (/home/ubuntu/anaconda3/envs/scFates-gpu/lib/python3.8/site-packages/cytopus/__init__.py)

I am wondering if I missed a critical step, but seems like the package and some dependencies were installed correctly.

Thank you for your help

This is an interesting project. I currently have breast cancer data and would like to use Cytopus to obtain factors and gene sets related to breast cancer. However, it seems that the Cytopus database only provides information about CRC (colorectal carcinoma) cells and NSCLC (non-small cell lung carcinoma) cells. Could you please provide guidance on how to obtain factors related to breast cancer?