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-started](https://microbiome.github.io/miaSim/articles/miaSim.html) -page. - -The package is based on the `(Tree)SummarizedExperiment` data -container that supports microbiome data analysis. The package -[homepage](https://microbiome.github.io/miaSim/) provides further -tutorials and references for the [implemented +This R/Bioconductor package provides tools to simulate (longitudinal) +time series data from popular models in microbial ecology. The +[homepage](https://microbiome.github.io/miaSim/) provides tutorials +and references for the [implemented models](https://microbiome.github.io/miaSim/reference/index.html): * Self-organised instability (SOI) @@ -35,7 +27,14 @@ models](https://microbiome.github.io/miaSim/reference/index.html): * Stochastic logistic model * Consumer-resource model +These methods can be used for _in silico_ studies of microbial +community dynamics or multi-omic or host-microbiome interactions. The +miaSim package supports the Bioconductor [multi-assay data science +framework](https://microbiome.github.io/OMA) for multi-omic data +integration and time series analysis, and utilizes the +`(Tree)SummarizedExperiment` data container. +[Getting started](https://microbiome.github.io/miaSim/articles/miaSim.html). ### miaSimShiny @@ -63,6 +62,13 @@ flow kind of approach. Development version should be done against the We are grateful to all [contributors](https://github.com/microbiome/miaSim/graphs/contributors). +This research has received funding from + + * the Horizon 2020 Programme of the European Union within the [FindingPheno project](https://www.findingpheno.eu/) under grant agreement No 952914. + * Research Council of Finland (grant 330887) + + +FindingPheno logo ### Citing the package @@ -74,12 +80,10 @@ Gao _et al._ (2023). Methods in Ecology and Evolution. DOI: For citation details, see R command `citation("miaSim")`. -# Code of conduct - -Please note that the project is released with a [Bioconductor Code of -Conduct](https://bioconductor.github.io/bioc_coc_multilingual/). -By contributing to this project, you agree to abide by its terms. - +**Code of conduct** Please note that the project is released with a +[Bioconductor Code of +Conduct](https://bioconductor.github.io/bioc_coc_multilingual/). By +contributing to this project, you agree to abide by its terms. [github-watch-badge]: https://img.shields.io/github/watchers/microbiome/miaSim.svg?style=social diff --git a/README.md b/README.md index 083e6a9..9faf7ca 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,6 @@ [![Gitter](https://badges.gitter.im/microbiome/mia.svg)](https://gitter.im/microbiome/miaverse) [![Watch on GitHub][github-watch-badge]][github-watch] [![Star on GitHub][github-star-badge]][github-star] - [![R-CMD-check](https://github.com/microbiome/miaSim/workflows/R-CMD-check/badge.svg)](https://github.com/microbiome/miaSim/actions) @@ -15,18 +14,10 @@ ## miaSim -This miaSim R/Bioconductor package can be used to simulate -(longitudinal) data for the benchmarking and analysis of quantitative -models of microbial communities. - -For installation and use, see the [Getting -started](https://microbiome.github.io/miaSim/articles/miaSim.html) -page. - -The package is based on the `(Tree)SummarizedExperiment` data -container that supports microbiome data analysis. The package -[homepage](https://microbiome.github.io/miaSim/) provides further -tutorials and references for the [implemented +This R/Bioconductor package provides tools to simulate (longitudinal) +time series data from popular models in microbial ecology. The +[homepage](https://microbiome.github.io/miaSim/) provides tutorials +and references for the [implemented models](https://microbiome.github.io/miaSim/reference/index.html): * Self-organised instability (SOI) @@ -36,7 +27,14 @@ models](https://microbiome.github.io/miaSim/reference/index.html): * Stochastic logistic model * Consumer-resource model +These methods can be used for _in silico_ studies of microbial +community dynamics or multi-omic or host-microbiome interactions. The +miaSim package supports the Bioconductor [multi-assay data science +framework](https://microbiome.github.io/OMA) for multi-omic data +integration and time series analysis, and utilizes the +`(Tree)SummarizedExperiment` data container. +[Getting started](https://microbiome.github.io/miaSim/articles/miaSim.html). ### miaSimShiny @@ -64,6 +62,13 @@ flow kind of approach. Development version should be done against the We are grateful to all [contributors](https://github.com/microbiome/miaSim/graphs/contributors). +This research has received funding from + + * the Horizon 2020 Programme of the European Union within the [FindingPheno project](https://www.findingpheno.eu/) under grant agreement No 952914. + * Research Council of Finland (grant 330887) + + +FindingPheno logo ### Citing the package @@ -75,12 +80,10 @@ Gao _et al._ (2023). Methods in Ecology and Evolution. DOI: For citation details, see R command `citation("miaSim")`. -# Code of conduct - -Please note that the project is released with a [Bioconductor Code of -Conduct](https://bioconductor.github.io/bioc_coc_multilingual/). -By contributing to this project, you agree to abide by its terms. - +**Code of conduct** Please note that the project is released with a +[Bioconductor Code of +Conduct](https://bioconductor.github.io/bioc_coc_multilingual/). By +contributing to this project, you agree to abide by its terms. [github-watch-badge]: https://img.shields.io/github/watchers/microbiome/miaSim.svg?style=social diff --git a/docs/404.html b/docs/404.html index 9202a7c..97fe97d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -7,8 +7,8 @@ Page not found (404) • miaSim - - + + @@ -25,7 +25,7 @@ miaSim - 1.7.8 + 1.9.1