https://github.com/campbio/musicatk
Mutational Signature Comprehensive Analysis Toolkit
Science Score: 23.0%
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
3 of 9 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary
Keywords from Contributors
Repository
Mutational Signature Comprehensive Analysis Toolkit
Basic Info
- Host: GitHub
- Owner: campbio
- Language: R
- Default Branch: master
- Size: 260 MB
Statistics
- Stars: 13
- Watchers: 3
- Forks: 9
- Open Issues: 15
- Releases: 8
Metadata Files
README.md
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Mutational Signature Comprehensive Analysis Toolkit
Introduction
A variety of exogenous exposures or endogenous biological processes can contribute to the overall mutational load observed in human tumors. Many different mutational patterns, or “mutational signatures”, have been identified across different tumor types. These signatures can provide a record of environmental exposure and can give clues about the etiology of carcinogenesis. The Mutational Signature Comprehensive Analysis Toolkit (musicatk) has utilities for extracting variants from a variety of file formats, contains multiple methods for discovery of novel signatures or prediction of known signatures, as well as many types of downstream visualizations for exploratory analysis. This package has the ability to parse and combine multiple motif classes in the mutational signature discovery or prediction processes. Mutation motifs include single base substitutions (SBS), double base substitutions (DBS), insertions (INS) and deletions (DEL).
Installation
Currently musicatk can be installed from on Bioconductor using the following code:
r
if (!requireNamespace("BiocManager", quietly=TRUE)){
install.packages("BiocManager")}
BiocManager::install("musicatk")
To install the latest version from Github, use the following code:
``` r if (!requireNamespace("devtools", quietly=TRUE)){ install.packages("devtools")}
library(devtools) install_github("campbio/musicatk") ```
The package can be loaded using the library command.
r
library(musicatk)
Tutorials
Detailed usage tutorials are available on the Camplab website under the 'Vignettes' drop-down.
Owner
- Name: campbio
- Login: campbio
- Kind: organization
- Website: camplab.net
- Twitter: camplab1
- Repositories: 12
- Profile: https://github.com/campbio
GitHub Events
Total
- Create event: 2
- Release event: 2
- Issues event: 2
- Watch event: 1
- Issue comment event: 1
- Push event: 13
- Gollum event: 3
- Pull request event: 18
- Fork event: 1
Last Year
- Create event: 2
- Release event: 2
- Issues event: 2
- Watch event: 1
- Issue comment event: 1
- Push event: 13
- Gollum event: 3
- Pull request event: 18
- Fork event: 1
Committers
Last synced: almost 3 years ago
Top Committers
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 22
- Total pull requests: 46
- Average time to close issues: 3 months
- Average time to close pull requests: 9 days
- Total issue authors: 7
- Total pull request authors: 6
- Average comments per issue: 0.86
- Average comments per pull request: 0.13
- Merged pull requests: 34
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- achevali (13)
- nathansahelijo (3)
- joshua-d-campbell (2)
- DarioS (1)
- bmeier011 (1)
- Acare (1)
- kevlumbus (1)
- kgeyer (1)
- ThomasGro (1)
- nqgurevich (1)
- avrajit (1)
Pull Request Authors
- nqgurevich (23)
- achevali (22)
- Gtnick1241 (7)
- nathansahelijo (6)
- BioTong (4)
- zeenu94 (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- NMF * depends
- R >= 4.0.0 depends
- BSgenome * imports
- BSgenome.Hsapiens.UCSC.hg19 * imports
- BSgenome.Hsapiens.UCSC.hg38 * imports
- BSgenome.Mmusculus.UCSC.mm10 * imports
- BSgenome.Mmusculus.UCSC.mm9 * imports
- Biostrings * imports
- ComplexHeatmap * imports
- GenomeInfoDb * imports
- GenomicFeatures * imports
- GenomicRanges * imports
- IRanges * imports
- MASS * imports
- MCMCprecision * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- TCGAbiolinks * imports
- TxDb.Hsapiens.UCSC.hg19.knownGene * imports
- TxDb.Hsapiens.UCSC.hg38.knownGene * imports
- VariantAnnotation * imports
- base * imports
- cluster * imports
- cowplot * imports
- data.table * imports
- decompTumor2Sig * imports
- deconstructSigs * imports
- dplyr * imports
- factoextra * imports
- ggplot2 * imports
- ggrepel * imports
- gridExtra * imports
- gtools * imports
- maftools * imports
- magrittr * imports
- matrixTests * imports
- methods * imports
- philentropy * imports
- plotly * imports
- rlang * imports
- shiny * imports
- shinyBS * imports
- shinyalert * imports
- shinybusy * imports
- shinydashboard * imports
- shinyjqui * imports
- shinyjs * imports
- sortable * imports
- stringi * imports
- stringr * imports
- tibble * imports
- tidyr * imports
- topicmodels * imports
- utils * imports
- uwot * imports
- withr * imports
- BiocStyle * suggests
- XVector * suggests
- covr * suggests
- knitr * suggests
- qpdf * suggests
- rmarkdown * suggests
- survival * suggests
- testthat * suggests
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
- actions/checkout v2 composite
- r-lib/actions/setup-r v1 composite
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