https://github.com/brentp/bpbio
basepair bio: a single binary with many useful genomics subtools.
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 (4.0%) to scientific vocabulary
Keywords
bam
cram
genomics
genomics-visualization
high-throughput-sequencing
structural-variation
Last synced: 5 months ago
·
JSON representation
Repository
basepair bio: a single binary with many useful genomics subtools.
Basic Info
Statistics
- Stars: 6
- Watchers: 2
- Forks: 2
- Open Issues: 4
- Releases: 2
Topics
bam
cram
genomics
genomics-visualization
high-throughput-sequencing
structural-variation
Created over 7 years ago
· Last pushed over 6 years ago
Metadata Files
Readme
License
README.md
bpbio: a single binary with a collection of sub-commands useful for genomics
- plot-sv-vcf: create a plot that shows the number of large and small variants separated by DEL/DUP/BND/INV for a multi-sample SV VCF. (idea from @ernfrid)
Libraries
- countstats: get median and percentiles for integers in constant space and little time.
- pedfile: ped (fam) file parsing and matching to VCF.
- duko: ergonomic embedded javascript via duktape and duktape-nim
- variexpr: simple expressions for filtering and labeling VCF records e.g.: denovo:kid.alts == 1 && mom.alts == 0 && dad.alts == 0 && kid.DP > 10
Abandoned
- homsv: look for depth changes in self-chains or homologous regions
- homsv-merge: merge output from homsv
Owner
- Name: Brent Pedersen
- Login: brentp
- Kind: user
- Location: Oregon, USA
- Twitter: brent_p
- Repositories: 220
- Profile: https://github.com/brentp
Doing genomics
GitHub Events
Total
Last Year
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Brent Pedersen | b****e@g****m | 53 |
| Joe Brown | b****m@g****m | 1 |
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 5
- Total pull requests: 1
- Average time to close issues: about 5 hours
- Average time to close pull requests: about 4 hours
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.2
- Average comments per pull request: 0.0
- Merged pull requests: 1
- 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
Top Authors
Issue Authors
- brentp (5)
Pull Request Authors
- brwnj (1)