https://github.com/bhklab/pdo_bme_ekgel
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bhklab
- License: apache-2.0
- Language: R
- Default Branch: master
- Size: 11.4 MB
Statistics
- Stars: 0
- Watchers: 7
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
PDOBMEEKGel
Introduction
This is a project to regenerate the RNAseq compariosn between PDOs clutured in two mediums in this paper: "Biomimetic hydrogel supports initiation and growth of patient-derived breast tumor organoids" citation's info to be added
The script for the analysis is written in R.
Dependencies:
These R packages need to be installed in order to run the analysis script: - Biobase - ggrepel - ggplot2 - ComplexHeatmap - circlize - DESeq2 - snowfall - GSA - piano
Reproducibility of the Analysis:
- Once the project is downloaded to the user computer, the user needs to navigate to the main directory of the project "PDOBMEEKGel-master".
- Inside the main directory, there is an R script file named "analysis.R". Running this script will regenerate the RNAseq compariosn between PDOs clutured in two mediums in this paper.
Important Note: the user needs to set the working directory inside the script file before running it, i.e. change the following code inside the script:
setwd("PDO_BME_EKGel") # set to path of cloned project in your machine
- Included in the project are:
1- RNAseq processed data for all PDOs clutured in different mediums, Data/UHN_BR_PDOs_hg38_kallisto_mixed.rda.
2- REACTOME genesets used for the pathway analysis, Data/c2.cp.reactome.v7.4.symbols.gmt.
Owner
- Name: BHKLAB
- Login: bhklab
- Kind: organization
- Location: Toronto, Ontario, Canada
- Website: http://www.pmgenomics.ca/bhklab/
- Repositories: 168
- Profile: https://github.com/bhklab
The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre
GitHub Events
Total
- Member event: 1
Last Year
- Member event: 1
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0