diff --git a/README.md b/README.md index 50c9b4dc7c5b54dd8bcedf9d29448008fe1d9ebc..ba1360b31534f104bf7f8170ff9f352166d6eaba 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,11 @@ # High-Throughput RNA-seq model fit + +- [Getting started](#getting-started) +- [Installation](#installation) +- [CRAN packages dependencies](#cran-packages-dependencies) +- [Docker](#docker) + ## Why use HTRfit HTRfit provides a robust statistical framework that allows you to investigate the essential experimental parameters influencing your ability to detect expression changes. Whether you're examining sequencing depth, the number of replicates, or other critical factors, HTRfit's computational simulation is your go-to solution. @@ -7,10 +13,13 @@ HTRfit provides a robust statistical framework that allows you to investigate th Furthermore, by enabling the inclusion of fixed effects, mixed effects, and interactions in your RNAseq data analysis, HTRfit provides the flexibility needed to conduct your differential expression analysis effectively. HTRfit is particularly adapted for the analysis of large number of samples, or highly multiplexed experiments. -- [Installation](#installation) -- [CRAN packages dependencies](#cran-packages-dependencies) -- [Docker](#docker) -- [Getting started](#getting-started) +## Getting started + +* [ Theory behind HTRfit ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/01-theoryBehindHtrfit.html) +* [ Simulation tutorial ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/02-tutorial.html) +* [ RNAseq analysis with HTRfit ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/03-rnaseq_analysis.html) +* [ Benchmarking HTRfit/DESeq2 ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/04-htrfit_vs_deseq2.html) + ## Installation @@ -92,10 +101,3 @@ docker run -it --rm \ A straightforward way to use **HTRfit** is to run it on a Virtual Machine (VM) through [Biosphere](https://biosphere.france-bioinformatique.fr/catalogue/). We recommend utilizing a VM that includes RStudio for an integrated development environment (IDE) experience. Biosphere VM resources can also be scaled according to your simulation needs. **HTRfit** can be installed using the [method A](#method-a). - -## Getting started - -* [ Theory behind HTRfit ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/theoryBehindHtrfit.html) -* [ Simulation tutorial ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/tutorial.html) -* [ Benchmarking HTRfit/DESeq2 ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/htrfit_vs_deseq2.html) -* [ RNAseq analysis with HTRfit ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/rnaseq_analysis.html) diff --git a/vignettes/theoryBehindHtrfit.Rmd b/vignettes/01-theoryBehindHtrfit.Rmd similarity index 100% rename from vignettes/theoryBehindHtrfit.Rmd rename to vignettes/01-theoryBehindHtrfit.Rmd diff --git a/vignettes/tutorial.Rmd b/vignettes/02-tutorial.Rmd similarity index 100% rename from vignettes/tutorial.Rmd rename to vignettes/02-tutorial.Rmd diff --git a/vignettes/rnaseq_analysis.Rmd b/vignettes/03-rnaseq_analysis.Rmd similarity index 100% rename from vignettes/rnaseq_analysis.Rmd rename to vignettes/03-rnaseq_analysis.Rmd diff --git a/vignettes/htrfit_vs_deseq2.Rmd b/vignettes/04-htrfit_vs_deseq2.Rmd similarity index 100% rename from vignettes/htrfit_vs_deseq2.Rmd rename to vignettes/04-htrfit_vs_deseq2.Rmd diff --git a/vignettes/list_var_object.Rmd b/vignettes/05-list_var_object.Rmd similarity index 100% rename from vignettes/list_var_object.Rmd rename to vignettes/05-list_var_object.Rmd diff --git a/vignettes/mock_rnaseq_object.Rmd b/vignettes/06-mock_rnaseq_object.Rmd similarity index 100% rename from vignettes/mock_rnaseq_object.Rmd rename to vignettes/06-mock_rnaseq_object.Rmd diff --git a/vignettes/rnaseq_notOnly.Rmd b/vignettes/07-rnaseq_notOnly.Rmd similarity index 100% rename from vignettes/rnaseq_notOnly.Rmd rename to vignettes/07-rnaseq_notOnly.Rmd