Package: DEploid.utils 0.0.1
Joe Zhu
DEploid.utils: 'DEploid' Data Analysis and Results Interpretation
'DEploid' (Zhu et.al. 2018 <doi:10.1093/bioinformatics/btx530>) is designed for deconvoluting mixed genomes with unknown proportions. Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting. This package provides R functions to support data analysis and results interpretation.
Authors:
DEploid.utils_0.0.1.tar.gz
DEploid.utils_0.0.1.tar.gz(r-4.5-noble)DEploid.utils_0.0.1.tar.gz(r-4.4-noble)
DEploid.utils_0.0.1.tgz(r-4.4-emscripten)DEploid.utils_0.0.1.tgz(r-4.3-emscripten)
DEploid.utils.pdf |DEploid.utils.html✨
DEploid.utils/json (API)
NEWS
| # Install 'DEploid.utils' in R: |
| install.packages('DEploid.utils', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 days agofrom:c418782bd9. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-linux-x86_64 | OK | Dec 19 2024 |
Exports:computeObsWSAFextractCoverageFromTxtextractCoverageFromVcfextractPLAFhaplotypePainterhistWSAFplotAltVsRefplotObsExpWSAFplotProportionsplotWSAFvsPLAF
Dependencies:clicolorspacecombinatfarvergluelabelinglifecyclemagrittrmunsellR6RColorBrewerRcpprlangscalesviridisLite
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute observed WSAF | computeObsWSAF |
| Extract read counts from plain text file | extractCoverageFromTxt |
| Extract VCF information | extractCoverageFromVcf |
| Extract PLAF | extractPLAF |
| Painting haplotype according the reference panel | haplotypePainter |
| WSAF histogram | histWSAF |
| Plot coverage | plotAltVsRef |
| Plot WSAF | plotObsExpWSAF |
| Plot proportions | plotProportions |
| Plot WSAF vs PLAF | plotWSAFvsPLAF |
