Science Score: 33.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
○DOI references
-
✓Academic publication links
Links to: ncbi.nlm.nih.gov -
✓Committers with academic emails
1 of 14 committers (7.1%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary
Keywords from Contributors
Repository
QDNAseq package for Bioconductor
Statistics
- Stars: 50
- Watchers: 6
- Forks: 30
- Open Issues: 38
- Releases: 1
Metadata Files
README.md
QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations
This repository contains source code for the R/Bioconductor package QDNAseq, which implements the QDNAseq method (Scheinin et al., 2014). For instructions on how to use QDNAseq, see the 'Introduction to QDNAseq' vignette, which also installed together with the package. Please remember to cite Scheinin et al. (2014) whenever using QDNAseq in your research.
Please use the official Bioconductor instructions to install QDNAseq;
r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("QDNAseq")
To analyze human data, the QDNAseq.hg19 package must be installed;
r
BiocManager::install("QDNAseq.hg19")
To analyze mouse data, the QDNAseq.mm10 package must be installed;
r
BiocManager::install("QDNAseq.mm10")
To install the devel versions of QDNAseq, QDNAseq.hg19, and QDNAseq.mm10, see the Bioconductor devel installation instruction.
References
- Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG and Ylstra B. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Research 24: 2022-2032, 2014. PMC4248318
GitHub repository and Bioconductor repository
This GitHub repository is (manually) kept in sync with the Bioconductor devel version of the QDNAseq package. More precisely, the master branch in this GitHub repository is in sync with what is on the Bioconductor git repository (e.g. git clone https://git.bioconductor.org/packages/QDNAseq). The source code previous versions is available via git tags, e.g. QDNAseq 1.21.1.
Owner
- Name: Tumor Genome Analysis Core
- Login: ccagc
- Kind: organization
- Location: Amsterdam, Netherlands
- Website: http://www.tgac.nl
- Repositories: 1
- Profile: https://github.com/ccagc
GitHub Events
Total
- Issues event: 7
- Watch event: 3
- Issue comment event: 5
- Fork event: 3
Last Year
- Issues event: 7
- Watch event: 3
- Issue comment event: 5
- Fork event: 3
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Henrik Bengtsson | hb@a****g | 147 |
| Daoud Sie | d****e@v****l | 25 |
| Ilari Scheinin | i****n@g****m | 21 |
| Nitesh Turaga | n****a@g****m | 14 |
| Dan Tenenbaum | d****a@f****g | 10 |
| Herve Pages | h****s@f****g | 4 |
| Hervé Pagès | h****s@f****g | 2 |
| J Wokaty | j****y@s****u | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| Dijk | e****1@C****l | 1 |
| Marc Carlson | m****n@f****g | 1 |
| Martin Morgan | m****n@f****g | 1 |
| Roel Kluin | r****n@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 99
- Total pull requests: 11
- Average time to close issues: 7 months
- Average time to close pull requests: 7 months
- Total issue authors: 52
- Total pull request authors: 7
- Average comments per issue: 2.67
- Average comments per pull request: 2.91
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 0
- Average time to close issues: 5 months
- Average time to close pull requests: N/A
- Issue authors: 6
- Pull request authors: 0
- Average comments per issue: 0.17
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- HenrikBengtsson (31)
- jiading (6)
- ilarischeinin (4)
- helaersr (3)
- sxv (3)
- RodrigoGM (2)
- lbeltrame (2)
- alexvasilikop (2)
- kojimak324 (2)
- hannesbecher (2)
- griffinfarrow (1)
- dakl (1)
- mmterpstra (1)
- vlshesketh (1)
- J-NYS (1)
Pull Request Authors
- HenrikBengtsson (3)
- RodrigoGM (2)
- sambrightman (2)
- marcjwilliams1 (1)
- ilarischeinin (1)
- edk360 (1)
- RoelKluin (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 62,136 total
- Total dependent packages: 4
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: QDNAseq
Quantitative DNA Sequencing for Chromosomal Aberrations
- Homepage: https://github.com/ccagc/QDNAseq
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/QDNAseq/inst/doc/QDNAseq.pdf
- License: GPL
-
Latest release: 1.44.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.1.0 depends
- Biobase >= 2.18.0 imports
- CGHbase >= 1.18.0 imports
- CGHcall >= 2.18.0 imports
- DNAcopy >= 1.32.0 imports
- GenomicRanges >= 1.20 imports
- IRanges >= 2.2 imports
- R.utils >= 2.9.0 imports
- Rsamtools >= 1.20 imports
- future.apply >= 1.8.1 imports
- graphics * imports
- matrixStats >= 0.60.0 imports
- methods * imports
- stats * imports
- utils * imports
- BSgenome >= 1.38.0 suggests
- BiocStyle >= 1.8.0 suggests
- GenomeInfoDb >= 1.6.0 suggests
- QDNAseq.hg19 * suggests
- QDNAseq.mm10 * suggests
- R.cache >= 0.13.0 suggests
- digest >= 0.6.20 suggests
- future >= 1.22.1 suggests
- parallelly >= 1.28.1 suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc master composite
- r-lib/actions/setup-r master composite
- r-lib/actions/setup-tinytex v1 composite
- actions/cache v1 composite
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc master composite
- r-lib/actions/setup-r master composite