Package: indelmiss 1.0.10

Utkarsh J. Dang

indelmiss: Insertion Deletion Analysis While Accounting for Possible Missing Data

Genome-wide gene insertion and deletion rates can be modelled in a maximum likelihood framework with the additional flexibility of modelling potential missing data using the models included within. These models simultaneously estimate insertion and deletion (indel) rates of gene families and proportions of "missing" data for (multiple) taxa of interest. The likelihood framework is utilized for parameter estimation. A phylogenetic tree of the taxa and gene presence/absence patterns (with data ordered by the tips of the tree) are required. See Dang et al. (2016) <doi:10.1534/genetics.116.191973> for more details.

Authors:Utkarsh J. Dang and G. Brian Golding

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indelmiss.pdf |indelmiss.html✨
indelmiss/json (API)
NEWS

# Install 'indelmiss' in R:
install.packages('indelmiss', repos = 'https://cloud.r-project.org')
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

1.00 score 154 downloads 6 exports 20 dependencies

Last updated 2 years agofrom:43874bb400. Checks:3 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
R-4.5-linux-x86_64OKMar 24 2025
R-4.4-linux-x86_64OKMar 24 2025

Exports:indelratesplot.indelmissplotpplotratesplottreeprint.indelmiss

Dependencies:apeclicpp11digestfastmatchgenericsglueigraphlatticelifecyclemagrittrMatrixnlmenumDerivphangornpkgconfigquadprogRcpprlangvctrs

Citation

To cite indelmiss in publications, please use:

Utkarsh J. Dang, Alison M. Devault, Tatum D. Mortimer, Caitlin S. Pepperell, Hendrik N. Poinar, G. Brian Golding (2016). Gene insertion deletion analysis while accounting for possible missing data. Genetics 204(2): 513--529.<doi:10.1534/genetics.116.191973>.

Corresponding BibTeX entry: 

  @Article{,
    title = {Gene insertion deletion analysis while accounting for
      possible missing data},
    author = {Utkarsh J. Dang and Alison M. Devault and Tatum D.
      Mortimer and Caitlin S. Pepperell and Hendrik N. Poinar and G.
      Brian Golding},
    journal = {Genetics},
    year = {2016},
    volume = {204},
    number = {2},
    pages = {513--529},
    doi = {10.1534/genetics.116.191973},
  }