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remove BMTME
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jpiaskowski committed Aug 27, 2023
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Expand Up @@ -234,7 +234,7 @@ There are many [GWAS packages on Bioconductor](https://bioconductor.org/packages

- `r pkg("PopVar")` has function for estimating population genetic variance from a biparental cross.

- *Multiple environments and traits*: `r pkg("BGGE")` conducts genomic prediction for continuous variables, focused on genotype-by-environment genomic selection models following the methods of [Jarquín 2014](https://doi.org/10.1007%2Fs00122-013-2243-1). The package `r pkg("BMTME")` builds genomic selection prediction models that can be expanded to multiple traits and environments using Bayesian models developed by Montesinos-Lopéz ([2016](https://doi.org/10.1534%2Fg3.116.032359), [2018a](https://doi.org/10.1534%2Fg3.118.200728), [2018b](https://doi.org/10.2134%2Fagronj2018.06.0362)). `r github("deruncie/megaLMM")` implements multivariate genomic prediction with very large numbers of traits (up to several thousand) using Bayesian genomic prediction models.
- *Multiple environments and traits*: `r pkg("BGGE")` conducts genomic prediction for continuous variables, focused on genotype-by-environment genomic selection models following the methods of [Jarquín 2014](https://doi.org/10.1007%2Fs00122-013-2243-1). `r github("deruncie/megaLMM")` implements multivariate genomic prediction with very large numbers of traits (up to several thousand) using Bayesian genomic prediction models.

- *Kinship and relatedness*: `r pkg("AGHmatrix", priority = "core")` provides extensive options for calculating pedigree and genomic relationships (additive and dominance). The `r pkg("pedigree")` packages provides functionality for ordering pedigrees, calculating and inverting the pedigree relationship matrix and other related tasks. `r pkg("statgenIBD")` can calculate IBD probabilities for biparental, three-way and four-way crosses. `r pkg("kinship2")` provides functions for manipulating and visualising pedigree-based kinship data.

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