Package: TE 0.3-0
TE: Insertion/Deletion Dynamics for Transposable Elements
Provides functions to estimate the insertion and deletion rates of transposable element (TE) families. The estimation of insertion rate consists of an improved estimate of the age distribution that takes into account random mutations, and an adjustment by the deletion rate. A hypothesis test for a uniform insertion rate is also implemented. This package implements the methods proposed in Dai et al (2018).
Authors:
TE_0.3-0.tar.gz
TE_0.3-0.zip(r-4.5)TE_0.3-0.zip(r-4.4)TE_0.3-0.zip(r-4.3)
TE_0.3-0.tgz(r-4.4-any)TE_0.3-0.tgz(r-4.3-any)
TE_0.3-0.tar.gz(r-4.5-noble)TE_0.3-0.tar.gz(r-4.4-noble)
TE_0.3-0.tgz(r-4.4-emscripten)TE_0.3-0.tgz(r-4.3-emscripten)
TE.pdf |TE.html✨
TE/json (API)
| # Install 'TE' in R: |
| install.packages('TE', repos = c('https://xdaiisu.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 6 years agofrom:b2de779278. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 10 2024 |
| R-4.5-win | OK | Nov 10 2024 |
| R-4.5-linux | OK | Nov 10 2024 |
| R-4.4-win | OK | Nov 10 2024 |
| R-4.4-mac | OK | Nov 10 2024 |
| R-4.3-win | OK | Nov 10 2024 |
| R-4.3-mac | OK | Nov 10 2024 |
Exports:EstDynamicsEstDynamics2MasterGeneMatrixModelnbLackOfFitKLPlotFamiliesSensitivityPlot
Dependencies:ashcliclustercolorspacefansifarverFNNggplot2gluegtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMASSMatrixmclustmgcvmulticoolmunsellmvtnormnlmepcaPPpillarpkgconfigpracmaR6rainbowRColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| LTR retrotransposons in _Aegilops tauschii_ | AetLTR |
| LTR retrotransposons in _Arabidopsis lyrata_ | AlyLTR |
| Estimate TE dynamics using mismatch data | EstDynamics EstDynamics2 |
| Implements the master gene model in Marchani et al (2009) | MasterGene |
| Implements the matrix model in Promislow et al (1999) | MatrixModel |
| Calcualte the KL divergence of a negative binomial fit to the mismatch data. | nbLackOfFitKL |
| Plot the age distributions or insertion rates for multiple families. | PlotFamilies |
| Print a TEfit or TEfit2 object | print.TEfit print.TEfit2 |
| Generate sensitivity plots | SensitivityPlot |
| TE: Insertion/Deletion Dynamics for Transposable Elements | TE-package TE |
