https://github.com/ctriermaansson/dnafusion
Identification of gene-fusions, including EML4-ALK
Science Score: 49.0%
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Repository
Identification of gene-fusions, including EML4-ALK
Basic Info
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- Stars: 4
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 0
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Metadata Files
README.md
DNAfusion 
An R/Bioconductor package to evaluate BAM files and identify genefusions, such as EML4-ALK
This package was created in order to increase the sensitivity of EML4-ALK detection from commercially available NGS products such as the AVENIO (Roche) pipeline. Paired-end sequencing of cfDNA generated BAM files can be used as input to discover EML4-ALK variants. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes. The package includes six functions. The output of the first function, EML4_ALK_detection(), is used to determine whether EML4-ALK is detected and serves as input for the next four exploratory functions characterizing the EML4-ALK variant. The last function EML4_ALK_analysis() combines the output of the exploratory functions. To serve as examples, this package includes BAM files representing the EML4-ALK positive cell line H3122 and the EML4-ALK negative cell line, HCC827.
Highlights
DNAfusion is under active development. In the future the package will include more genefusions such as ROS1 and RET, as well as other ALK fusionpartners.
Installation
Use devtools to install the most recent version of DNAfusion from the GitHub repository.
```R if (!require(devtools)) install.packages('devtools') library(devtools)
devtools::installgithub("CTrierMaansson/DNAfusion", buildvignettes = TRUE) library(DNAfusion)
```
Alternatively, install DNAfusion published at Bioconductor.
```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("DNAfusion") library(DNAfusion)
```
Vignettes
See the documentation at https://github.com/CTrierMaansson/DNAfusion/tree/main/vignettes
Alternatively, the vignettes can be browsed in Rstudio with
R
browseVignettes("DNAfusion")
This requires build_vignettes = TRUE during installation with github
Citation
If you use DNAfusion in published research please cite:
Christoffer Trier Maansson, Emma Roger Andersen, Maiken Parm Ulhoi, Peter Meldgaard, Boe Sandahl Sorensen (2022). DNAfusion: An R/Bioconductor package to identify gene fusions. R package version 1.2.0 https://github.com/CTrierMaansson/DNAfusion
Maansson CT, Andersen ER, Ulhoi MP, Meldgaard P, Sorensen BS. “DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies.” BMC Bioinformatics, 2023, 24:131, doi:10.1186/s12859-023-05259-3.
Owner
- Name: Christoffer Trier Månsson
- Login: CTrierMaansson
- Kind: user
- Location: Aarhus University Hospital
- Website: https://www.linkedin.com/in/christoffer-maansson/
- Twitter: triermaansson1
- Repositories: 3
- Profile: https://github.com/CTrierMaansson
PhD student at AUH studying blood based biomarkers in lung cancer patients. My main focuses are epigenetic features in liquid biopsies and NGS.
GitHub Events
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- Push event: 7
Last Year
- Push event: 7
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| CTrierMaansson | c****m@c****k | 146 |
| J Wokaty | j****y@s****u | 10 |
| A Wokaty | a****y@s****u | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 1
- Average time to close issues: about 20 hours
- Average time to close pull requests: 2 minutes
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 6.0
- 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
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- Issue authors: 0
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- Average comments per issue: 0
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- Bot issues: 0
- Bot pull requests: 0
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- CTrierMaansson (1)
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 5,543 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: DNAfusion
Identification of gene fusions using paired-end sequencing
- Homepage: https://github.com/CTrierMaansson/DNAfusion
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/DNAfusion/inst/doc/DNAfusion.pdf
- License: GPL-3
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Latest release: 1.10.0
published 10 months ago
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Maintainers (1)
Dependencies
- R >= 4.2.0 depends
- dplyr * depends
- GenomicRanges * imports
- IRanges * imports
- Rsamtools * imports
- bamsignals * imports
- BiocStyle * suggests
- devtools * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
- usethis * suggests