Package: denovolyzeR 0.2.0
denovolyzeR: Statistical Analyses of De Novo Genetic Variants
An integrated toolset for the analysis of de novo (sporadic) genetic sequence variants. denovolyzeR implements a mutational model that estimates the probability of a de novo genetic variant arising in each human gene, from which one can infer the expected number of de novo variants in a given population size. Observed variant frequencies can then be compared against expectation in a Poisson framework. denovolyzeR provides a suite of functions to implement these analyses for the interpretation of de novo variation in human disease.
Authors:
denovolyzeR_0.2.0.tar.gz
denovolyzeR_0.2.0.zip(r-4.5)denovolyzeR_0.2.0.zip(r-4.4)denovolyzeR_0.2.0.zip(r-4.3)
denovolyzeR_0.2.0.tgz(r-4.4-any)denovolyzeR_0.2.0.tgz(r-4.3-any)
denovolyzeR_0.2.0.tar.gz(r-4.5-noble)denovolyzeR_0.2.0.tar.gz(r-4.4-noble)
denovolyzeR_0.2.0.tgz(r-4.4-emscripten)denovolyzeR_0.2.0.tgz(r-4.3-emscripten)
denovolyzeR.pdf |denovolyzeR.html✨
denovolyzeR/json (API)
NEWS
| # Install 'denovolyzeR' in R: |
| install.packages('denovolyzeR', repos = c('https://jamesware.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jamesware/denovolyzer/issues
- autismDeNovos - De novo variants found in 1,078 autism trios
- fmrpGenes - FMRP genes
Last updated 8 years agofrom:badc99f8d6. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 26 2024 |
| R-4.5-win | OK | Oct 26 2024 |
| R-4.5-linux | OK | Oct 26 2024 |
| R-4.4-win | OK | Oct 26 2024 |
| R-4.4-mac | OK | Oct 26 2024 |
| R-4.3-win | OK | Oct 26 2024 |
| R-4.3-mac | OK | Oct 26 2024 |
Exports:denovolyzedenovolyzeByClassdenovolyzeByGenedenovolyzeMultiHitsviewProbabilityTable
Dependencies:clidplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigplyrR6Rcppreshape2rlangstringistringrtibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| de novo variants found in 1,078 autism trios | autismDeNovos |
| Evaluates burden of _de novo_ variation against expectation | denovolyze denovolyzeByClass denovolyzeByGene |
| Determine significance of genes with multiple _de novos_ | denovolyzeMultiHits |
| A package for the analysis of _de novo_ sequencing variants | denovolyzeR-package denovolyzeR |
| FMRP genes | fmrpGenes |
| Checks input for errors | parseInput |
| Permutes x variants across a genelist, and counts genes with multiple hits | PermuteMultiHits |
| Displays underlying _de novo_ probability tables | viewProbabilityTable |
