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Initial implementation of Devon's analysis #116

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Initial implementation of Devon's analysis #116

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ac91512
Add new query for Devon's analysis
cthoyt Sep 15, 2022
dee62ce
Update queries
cthoyt Sep 15, 2022
6f1c485
Update devon_analysis.py
cthoyt Sep 15, 2022
3eec446
Update devon_analysis.py
cthoyt Sep 15, 2022
914cd2a
Add second and third analyses
cthoyt Sep 22, 2022
5cb93be
Add more analysis
cthoyt Feb 21, 2023
aba2326
Reorganize files for vartika analysis
cthoyt Apr 10, 2023
10c0a61
Update vartika analysis
cthoyt Jul 19, 2023
0c23748
Update devon_analysis.py
cthoyt Jul 19, 2023
3706560
Update devon_analysis.py
cthoyt Aug 7, 2023
bb8a77a
Update devon_analysis.py
cthoyt Aug 7, 2023
b876bd1
Add density query and extra logging
cthoyt Aug 7, 2023
45e2e8a
Create README.md
cthoyt Aug 7, 2023
724e52e
Update density analysis to have query comparison
cthoyt Aug 7, 2023
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Empty file added src/indra_cogex/analyses/__init__.py
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Empty file added src/indra_cogex/analyses/devon/__init__.py
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501 changes: 501 additions & 0 deletions src/indra_cogex/analyses/devon/devon/Exploratory_query.csv
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23 changes: 23 additions & 0 deletions src/indra_cogex/analyses/devon/devon/MAPK_downstream.csv
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12 changes: 12 additions & 0 deletions src/indra_cogex/analyses/devon/devon/README.md
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# Devon Data

| Attribute | Value |
|---------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Publication | [Leduc *et al.*, 2022](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02817-5) |
| Access | https://scp.slavovlab.net/Leduc_et_al_2022#raw_data |
| Description | Single cell (SC) mass spectrometry-based proteomics experiments using Melanoma and Monocyte cell lines. The main goal of the experiment was to show how their new SC workflow (nPOP) works. Included markers for a small subset of cells that were in different stages of the cell cycle. |
| Acquisition method | DDA |
| Labeling type | TMT |
| Replicates | 1556 cells |
| Number of proteins ID | 2844 (avg of 997 per cell) |
| Spectral processing tool used for identification and quantification | MaxQuant |
2,845 changes: 2,845 additions & 0 deletions src/indra_cogex/analyses/devon/devon/example_data.csv
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