Science Score: 36.0%
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
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.5%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: Liubuntu
- Language: R
- Default Branch: master
- Size: 4.61 MB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 1
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
SeqSQC
SeqSQC is a bioconductor package for sample-level quality check in next generation sequencing (NGS) study. It is designed to automate and accelerate the sample cleaning of NGS data in any scale, including identifying problematic samples with high missing rate, gender mismatch, contamination, abnormal inbreeding coefficient, cryptic relatedness, and discordant population information. SeqSQC takes Variant Calling Format (VCF) files and sample annotation file containing sample population and gender information as input and report problematic samples to be removed from downstream analysis. Through incorporation a benchmark data assembled from the 1000 Genomes Project, it can accommodate NGS study of small sample size and low number of variants.
Owner
- Name: Qian Liu
- Login: Liubuntu
- Kind: user
- Location: Buffalo
- Company: Roswell Park Comprehensive Cancer Center
- Website: https://www.roswellpark.org/qian-liu
- Twitter: QianLiu28878838
- Repositories: 3
- Profile: https://github.com/Liubuntu
Assistant Professor in Department of Biostats & Bioinfo Alumni @Bioconductor Core Team
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Qian Liu | q****7@b****u | 26 |
| Nitesh Turaga | n****a@g****m | 4 |
| Qian Liu | l****c@g****m | 3 |
| liubuntu | hq@l****n | 2 |
| vobencha | v****a@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| LiNk-NY | m****9@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: over 3 years
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 1.0
- 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
- tinu-t (1)
- seifudd (1)
Pull Request Authors
- hubentu (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: SeqSQC
A bioconductor package for sample quality check with next generation sequencing data
- Homepage: https://github.com/Liubuntu/SeqSQC
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/SeqSQC/inst/doc/SeqSQC.pdf
- License: GPL-3
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Latest release: 1.30.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- ExperimentHub >= 1.3.7 depends
- R >= 3.4 depends
- SNPRelate >= 1.10.2 depends
- GGally * imports
- GenomicRanges * imports
- IRanges * imports
- RColorBrewer * imports
- S4Vectors * imports
- e1071 * imports
- gdsfmt * imports
- ggplot2 * imports
- methods * imports
- rbokeh * imports
- reshape2 * imports
- rmarkdown * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- testthat * suggests