PureCN
Copy number calling and variant classification using targeted short read sequencing
Science Score: 49.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 31 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 18 committers (5.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Copy number calling and variant classification using targeted short read sequencing
Basic Info
- Host: GitHub
- Owner: lima1
- License: artistic-2.0
- Language: R
- Default Branch: devel
- Homepage: https://bioconductor.org/packages/devel/bioc/html/PureCN.html
- Size: 19 MB
Statistics
- Stars: 138
- Watchers: 6
- Forks: 33
- Open Issues: 47
- Releases: 0
Topics
Metadata Files
README.md
PureCN
A tool developed for tumor-only diagnostic sequencing using hybrid-capture protocols. It provides copy number adjusted for purity and ploidy and can classify mutations by somatic status and clonality. It requires a pool of process-matched normals for coverage normalization and artifact filtering. PureCN was parameterized using large collections of diverse samples, ranging from low coverage whole-exome to ultra-deep sequenced plasma gene-panels.
Installation
To install this package, start R and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PureCN")
If your R/Bioconductor version is outdated, this will install an old and unsupported version.
For outdated R/Bioconductor versions, you can try backporting the latest stable version (this should work fine for Bioconductor 3.3 and later):
BiocManager::install("lima1/PureCN", ref = "RELEASE_3_21")
If you want the latest and greatest from the developer branch:
BiocManager::install("lima1/PureCN")
To get the lastest stable version from Conda (unstable is currently only available from GitHub directly):
conda install -c bioconda bioconductor-purecn=2.12.0
A Dockerhub image of the latest stable version with recommended dependencies such as GenomicsDB and GATK 4 pre-installed:
docker pull markusriester/purecn:latest
Tutorials
To get started:
vignette("Quick", package = "PureCN")
For the R package and more detailed information:
vignette("PureCN", package = "PureCN")
These tutorials are also available on the Bioconductor project page (devel, stable).
Bugs
Before posting a bug report:
- update to the latest version
- confirm with sessionInfo() that the latest version is used
- if this is a first PureCN attempt, closely follow the Quick vignette (devel, stable)
- make sure that the issue is not covered in the Support section of the main vignette
Papers
Main paper describing the likelihood model:
Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D and Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for Biology and Medicine, 11, pp. 13. doi: 10.1186/s13029-016-0060-z.
Validation paper, including description of novel additions, such as off-target support, tangent normalization and tweaks to the likelihood model:
Oh S, Geistlinger L, Ramos M, Morgan M, Waldron L, Riester M (2020). Reliable analysis of clinical tumor-only whole exome sequencing data. JCO Clinical Cancer Informatics. doi: 10.1200/CCI.19.00130;
bioRxiv. doi: 10.1101/552711
Selected citations
Pereira et al. (2021). "Cell-free DNA captures tumor heterogeneity and driver alterations in rapid autopsies with pre-treated metastatic cancer". Nature Communications. doi: 10.1038/s41467-021-23394-4.
Dummer et al. (2020). "Combined PD-1, BRAF and MEK inhibition in advanced BRAF-mutant melanoma: safety run-in and biomarker cohorts of COMBI-i". Nature Medicine. doi: 10.1038/s41591-020-1082-2.
Bertucci et al. (2019). "Genomic characterization of metastatic breast cancers". Nature. doi: 10.1038/s41586-019-1056-z.
Dagogo-Jack et al. (2018). "Tracking the evolution of resistance to ALK tyrosine kinase inhibitors through longitudinal analysis of circulating tumor DNA". JCO Precision Oncology. doi: 10.1200/PO.17.00160.
Orlando et al. (2018). "Genetic mechanisms of target antigen loss in CAR19 therapy of acute lymphoblastic leukemia". Nature Medicine. doi: 10.1038/s41591-018-0146-z.
Pal et al. (2018). "Efficacy of BGJ398, a fibroblast growth factor receptor 1-3 inhibitor, in patients with previously treated advanced urothelial carcinoma with FGFR3 alterations". Cancer Discovery. doi: 10.1158/2159-8290.CD-18-0229.
Pitt et al. (2018). "Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features". Nature Communications. doi: 10.1038/s41467-018-06616-0.
Owner
- Name: Markus Riester
- Login: lima1
- Kind: user
- Location: Boston
- Company: Novartis Institutes for BioMedical Research
- Repositories: 6
- Profile: https://github.com/lima1
GitHub Events
Total
- Issues event: 20
- Watch event: 9
- Delete event: 2
- Issue comment event: 48
- Push event: 19
- Pull request event: 6
- Fork event: 3
- Create event: 1
Last Year
- Issues event: 20
- Watch event: 9
- Delete event: 2
- Issue comment event: 48
- Push event: 19
- Pull request event: 6
- Fork event: 3
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Markus Riester | m****r@n****m | 930 |
| lima1 | m****r@g****e | 218 |
| Nitesh Turaga | n****a@g****m | 14 |
| Dan Tenenbaum | d****a@f****g | 4 |
| Andrew J. Rech | r****h@r****o | 4 |
| Herve Pages | h****s@f****g | 4 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
| Boyang Zhao | b****o@q****m | 2 |
| vobencha | v****a@g****m | 2 |
| chapmanb | c****b@5****m | 2 |
| LiNk-NY | m****9@g****m | 1 |
| Martin Morgan | m****n@f****g | 1 |
| Hervé Pagès | h****b@g****m | 1 |
| aoles | a****s@g****m | 1 |
| lshep | l****d@r****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 95
- Total pull requests: 19
- Average time to close issues: about 1 month
- Average time to close pull requests: 4 days
- Total issue authors: 54
- Total pull request authors: 5
- Average comments per issue: 3.62
- Average comments per pull request: 0.32
- Merged pull requests: 19
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 14
- Pull requests: 6
- Average time to close issues: 9 days
- Average time to close pull requests: about 4 hours
- Issue authors: 10
- Pull request authors: 3
- Average comments per issue: 2.43
- Average comments per pull request: 0.17
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jennyp76 (5)
- maxanes (4)
- MaryGoAround (4)
- WangKang-Leo (4)
- lmanchon (4)
- lima1 (4)
- akaviaLab (4)
- gagank4911 (3)
- waemm (3)
- tinyheero (3)
- sleyn (3)
- Moe94 (2)
- ntran95 (2)
- jberg1999 (2)
- kristianunger (2)
Pull Request Authors
- lima1 (12)
- tinyheero (2)
- nspies-carisls (2)
- lbeltrame (2)
- ddrichel (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 33,339 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
bioconductor.org: PureCN
Copy number calling and SNV classification using targeted short read sequencing
- Homepage: https://github.com/lima1/PureCN
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/PureCN/inst/doc/PureCN.pdf
- License: Artistic-2.0
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Latest release: 2.14.1
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- DNAcopy * depends
- R >= 3.5.0 depends
- VariantAnnotation >= 1.14.1 depends
- genomicsdb >= 0.0.3 enhances
- Biobase * imports
- BiocGenerics * imports
- Biostrings * imports
- GenomeInfoDb * imports
- GenomicFeatures * imports
- GenomicRanges >= 1.20.3 imports
- IRanges >= 2.2.1 imports
- Matrix * imports
- RColorBrewer * imports
- Rsamtools * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- VGAM * imports
- data.table * imports
- futile.logger * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- gridExtra * imports
- mclust * imports
- methods * imports
- rhdf5 * imports
- rtracklayer * imports
- stats * imports
- tools * imports
- utils * imports
- BiocParallel * suggests
- BiocStyle * suggests
- PSCBS * suggests
- R.utils * suggests
- TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
- copynumber * suggests
- covr * suggests
- jsonlite * suggests
- knitr * suggests
- markdown * suggests
- optparse * suggests
- org.Hs.eg.db * suggests
- rmarkdown * suggests
- testthat * suggests