screenCounter
Get barcode counts from functional genomics screens
Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
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○.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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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.5%) to scientific vocabulary
Keywords from Contributors
Repository
Get barcode counts from functional genomics screens
Basic Info
- Host: GitHub
- Owner: crisprVerse
- License: mit
- Language: C++
- Default Branch: devel
- Homepage: https://bioconductor.org/packages/screenCounter
- Size: 488 KB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
Counting barcodes in functional screens
|Environment|Status|
|---|---|
|BioC-release|
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|BioC-devel|
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screenCounter quantifies the frequency of barcodes in sequencing data from functional screens, yielding a count matrix that can be subjected to further statistical analyses, e.g., with edgeR and contemporaries. We support single barcode, combinatorial barcode and dual barcode designs, where each construct is assumed to have constant sequence(s) flanking one or more variable regions of known length. The package also provides options for mismatches, strand-specific searching and parallelization via BiocParallel.
For users: check out the documentation at the Bioconductor landing page for installation and usage instructions.
For developers: this R package is just a wrapper around the kaori C++ library that does the heavy lifting. Pull requests for new barcode designs should be made in kaori first, and then propagated back down to screenCounter.
Owner
- Name: crisprVerse
- Login: crisprVerse
- Kind: organization
- Email: fortin946@gmail.com
- Repositories: 4
- Profile: https://github.com/crisprVerse
Bioconductor ecosystem for CRISPR gRNA design
GitHub Events
Total
- Push event: 1
- Fork event: 1
- Create event: 1
Last Year
- Push event: 1
- Fork event: 1
- Create event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Aaron Lun | l****n@g****m | 283 |
| LTLA | i****s@g****m | 26 |
| fortinj2 | f****e@g****m | 5 |
| J Wokaty | j****y | 2 |
| Jean-Philippe Fortin - Regular | f****2@n****m | 1 |
| fortinj2 | f****2@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: almost 2 years ago
All Time
- Total issues: 4
- Total pull requests: 2
- Average time to close issues: 2 days
- Average time to close pull requests: 1 day
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 3.5
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: 1 day
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 6.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- j-andrews7 (3)
- williambakhache (1)
Pull Request Authors
- LTLA (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 4,861 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: screenCounter
Counting Reads in High-Throughput Sequencing Screens
- Homepage: https://github.com/crisprVerse/screenCounter
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/screenCounter/inst/doc/screenCounter.pdf
- License: MIT + file LICENSE
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Latest release: 1.8.0
published about 1 year ago