2015_bray_gigascience-data
Bray GigaScience data
https://github.com/broadinstitute/2015_bray_gigascience-data
Science Score: 52.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Committers with academic emails
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✓Institutional organization owner
Organization broadinstitute has institutional domain (www.broadinstitute.org) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.5%) to scientific vocabulary
Repository
Bray GigaScience data
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: master
- Size: 4.18 MB
Statistics
- Stars: 0
- Watchers: 9
- Forks: 0
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
Bray GigaScience data
Download the data
- Clone the repo.
bash
git clone https://github.com/broadinstitute/2015_Bray_GigaScience-data.git
bash
git lfs pull
- Download the profiles from S3.
bash
dvc pull
Re-generate the data
To reproduce the profiles in this repo, run the profiling-recipe. But run the following two steps to create metadata files and fix well position names
Create metadata files
Install the conda environment in create_metadata/environment.yml and run the notebook create_metadata.ipynb to create all the metadata and platemap files.
Fix well names
Use the same conda enviroment as above and run fix_well_position.py to change the well names from a01 to A01 in the aggregated profiles. Run the recipe only after fixing the names of the wells.
Notes
quality_control step was not run because the load_data.csv.gz files did not have the column Metadata_Row. This column could be created and the quality_control step can be run later.
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this template, please cite it as below." authors: - family-names: "Chandrasekaran" given-names: "Srinivas Niranj" orcid: "https://orcid.org/0000-0001-8874-9988" - family-names: "Way" given-names: "Gregory" orcid: "https://orcid.org/0000-0002-0503-9348" - family-names: "Carpenter" given-names: "Anne" orcid: "https://orcid.org/0000-0003-1555-8261" - family-names: "Singh" given-names: "Shantanu" orcid: "https://orcid.org/0000-0003-3150-3025" title: "Broad Institute Imaging Platform Profiling Template" url: "https://github.com/cytomining/profiling-template"
GitHub Events
Total
- Issues event: 2
- Issue comment event: 1
Last Year
- Issues event: 2
- Issue comment event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Niranj | s****j@g****m | 18 |
| Ubuntu | u****u@i****l | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 3
- Total pull requests: 5
- Average time to close issues: about 9 hours
- Average time to close pull requests: about 4 hours
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 2.33
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: about 17 hours
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jasperhyp (1)
- shntnu (1)
- niranjchandrasekaran (1)
Pull Request Authors
- niranjchandrasekaran (5)