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SparseSignatures

Extracting mutational signatures via LASSO. The manuscript of the method is published on PLOS Computational Biology and available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009119

https://github.com/danro9685/sparsesignatures

Science Score: 13.0%

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Last synced: 11 months ago · JSON representation

Repository

Extracting mutational signatures via LASSO. The manuscript of the method is published on PLOS Computational Biology and available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009119

Basic Info
Statistics
  • Stars: 11
  • Watchers: 3
  • Forks: 4
  • Open Issues: 0
  • Releases: 15
Created about 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

SparseSignatures

| Branch | Status | | --- | --- | | master | R-CMD-check-bioc | | development | R-CMD-check-bioc |

Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient's tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient.

A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.

Owner

  • Name: Daniele Ramazzotti
  • Login: danro9685
  • Kind: user
  • Location: Milano, Italy
  • Company: University of Milano-Bicocca, Milano, Italy

Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy

GitHub Events

Total
  • Release event: 2
  • Watch event: 1
  • Push event: 10
  • Create event: 2
Last Year
  • Release event: 2
  • Watch event: 1
  • Push event: 10
  • Create event: 2

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 369
  • Total Committers: 3
  • Avg Commits per committer: 123.0
  • Development Distribution Score (DDS): 0.144
Past Year
  • Commits: 39
  • Committers: 2
  • Avg Commits per committer: 19.5
  • Development Distribution Score (DDS): 0.026
Top Committers
Name Email Commits
danro9685 d****i@y****m 316
avantikalal a****0@g****m 30
luca-dex l****o@g****m 23

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 12,951 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: SparseSignatures

SparseSignatures

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 12,951 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 5.1%
Stargazers count: 8.5%
Average: 15.4%
Downloads: 63.6%
Maintainers (1)
luca.desano@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • NMF * depends
  • R >= 4.1.0 depends
  • BSgenome * imports
  • Biostrings * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • data.table * imports
  • ggplot2 * imports
  • gridExtra * imports
  • nnlasso * imports
  • nnls * imports
  • parallel * imports
  • reshape2 * imports
  • BSgenome.Hsapiens.1000genomes.hs37d5 * suggests
  • BiocGenerics * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • testthat * suggests
.github/workflows/check-development.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite
.github/workflows/check-master.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite