Package: SparseSignatures 2.17.0
Luca De Sano
SparseSignatures: SparseSignatures
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.
Authors:
SparseSignatures_2.17.0.tar.gz
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SparseSignatures.pdf |SparseSignatures.html✨
SparseSignatures/json (API)
NEWS
| # Install 'SparseSignatures' in R: |
| install.packages('SparseSignatures', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/danro9685/sparsesignatures/issues
- background - Germline replication error
- background2 - COSMIC replication error
- cv_example - Example of results obtained with the function nmf.LassoCV on the counts input from Nik-Zainal, Serena, et al. (2016).
- imported_data - Example of imported data from Nik-Zainal, Serena, et al. (2016).
- lambda_range_example - Example of results obtained with the function evaluate.lambda.range on the counts input from Nik-Zainal, Serena, et al. (2016).
- mutation_categories - Trinucleotides mutation categories
- nmf_LassoK_example - Example of results obtained with the function nmf.LassoK on the counts input from Nik-Zainal, Serena, et al. (2016).
- patients - Point mutations for 560 breast tumors
- ssm560_reduced - A reduced version of the point mutations for 560 breast tumors in the format compatible with the import function
- starting_betas_example - Example of results obtained with the function starting.betas.estimation on the counts input from Nik-Zainal, Serena, et al. (2016).
On BioConductor:SparseSignatures-2.17.0(bioc 3.21)SparseSignatures-2.16.0(bioc 3.20)
biomedicalinformaticssomaticmutation
Last updated 23 days agofrom:f2c94d341a. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win | WARNING | Nov 01 2024 |
| R-4.5-linux | WARNING | Nov 01 2024 |
| R-4.4-win | WARNING | Nov 01 2024 |
| R-4.4-mac | NOTE | Nov 01 2024 |
| R-4.3-win | WARNING | Nov 01 2024 |
| R-4.3-mac | NOTE | Nov 01 2024 |
Exports:import.trinucleotides.countslambdaRangeAlphaEvaluationlambdaRangeBetaEvaluationnmfLassonmfLassoBootstrapnmfLassoCVpatients.plotsigAssignmentCVsigAssignmentEvaluationsigAssignmentLassosignatures.plotstartingBetaEstimation
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsBSgenomecliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestdoParallelfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridBasegridExtragtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeNMFnnlassonnlsopensslpillarpkgconfigplyrR6RColorBrewerRcppRCurlregistryreshape2restfulrRhpcBLASctlRhtslibrjsonrlangrngtoolsRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
