https://github.com/rrrlw/mir_combo_targeting
Companion code for the paper: "Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma"
https://github.com/rrrlw/mir_combo_targeting
Last synced: 5 months ago
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Companion code for the paper: "Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma"
- Host: GitHub
- URL: https://github.com/rrrlw/mir_combo_targeting
- Owner: rrrlw
- Created: 2020-10-01T23:39:45.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2020-09-22T01:35:33.000Z (almost 6 years ago)
- Last Synced: 2025-06-03T02:56:26.573Z (about 1 year ago)
- Size: 17.6 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# MiR_Combo_Targeting
Companion code for the paper: "Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma"
You can find the pre-print for this analysis here.https://www.biorxiv.org/content/10.1101/854695v1
If you have any questions regarding how to run this pipeline on your device/ use it for your research,
feel free to shoot me an email at davis.weaver@case.edu.
## Here is the general flow:
1. Main_EWS_miR (by calling the functions in NP_pipeline_MiR and NP_Funcs_MiR) converts the processed RNA sequencing data and the biogrid PPI into cell signaling networks and does in-silico repression experiments to generate a list of protein targets. This step made use of ~20 cores of an HPC. Attempting to do it on a laptop or desktop would likely take a period of days to weeks.
2. miR_Analysis_Ewing (by calling the functions in miR_Analysis_Functions) processes the results of Main_EWS_miR and evaluates miR cocktails to identify optimal 3 miR combinations.
3. miR_Figs_Ewing produces all the figures and tables from the paper using the output of both miR_Analysis_Ewing and Main_EWS_miR.
## Dependencies:
Package dependencies are at the top of each script.
Each script also requires data files to run.
1. Main_EWS_miR.R
* rld_counts.csv
* BIOGRID-ORGANISM-Homo_sapiens-3.5.171.tab2.txt
2. miR_Analysis_Ewing.R
* EwingsDatasetFinal.csv
* all_miRNA_targets.rda
* Census_allMon_2019.csv
* Housekeeping_GenesHuman.csv
3. miR_Figs_Ewing
* Protein_RNA_correlation.csv
Create a folder in the folder where you store the code called "data_files". Download these 7 dependencies do that folder and then it should (hopefully) all go.