updt news & readme

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NEWS.md

+# CHANGES IN HTRfit VERSION 2.1
+
+* Improved Documentation: Clearer and more comprehensive information on HTRfit functionalities and usage.
+* Additional Metrics: Added RMSE for enhanced model evaluation.
+* Additional plot: Violin plot to measure proximity between actual and estimate for random effects.
+* Improved Flexibility: Ability to combine various genes behavior with `combine_mock()`
+* User experience: More informative messages.
+* R 4.4.0 Compatible: Fully supports the latest R version.
+
 # CHANGES IN HTRfit VERSION 2.0.0
 
 * Improved Documentation: Clearer and more comprehensive information on HTRfit functionalities and usage.

README.md

@@ -11,7 +11,6 @@ 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.
 
-
 ## Getting started
 
 Our documentation includes a few example applications showing how to use our package:
@@ -20,7 +19,14 @@ Our documentation includes a few example applications showing how to use our pac
 * [ 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)
+* [ Not only RNAseq ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/07-rnaseq_notOnly.html)
+
+## Advance user
 
+* [ FAQ ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/09-FAQ.html)
+* [ About evaluation metrics ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/08-evaluationMetrics.html)
+* [ list_var object ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/05-list_var_object.html)
+* [ mock_rnaseq object ](https://htrfit-lbmc-yvertlab-vortex-plasticity-mutation-477701eb488dfd9.gitbiopages.ens-lyon.fr/articles/06-mock_rnaseq_object.html)
 
 ## Installation
 
@@ -38,8 +44,8 @@ remotes::install_git("https://gitbio.ens-lyon.fr/aduvermy/HTRfit")
 You also have the option to download a release directly from the [HTRfit release page](https://gitbio.ens-lyon.fr/aduvermy/HTRfit/-/tags). Once you've downloaded the release, simply launch following command.
 
 ```r
-## -- Example using the HTRfit-v2.0.0 release
-install.packages('HTRfit-v2.0.0.tar.gz', repos = NULL, type='source')
+## -- Example using the HTRfit-v2.1 release
+install.packages('HTRfit-v2.1.tar.gz', repos = NULL, type='source')
 
 ```
 
@@ -65,8 +71,8 @@ BiocManager::install('DESeq2', update = FALSE)
 We have developed [Docker images](https://hub.docker.com/r/ruanad/htrfit/tags) to simplify the package's utilization.
 
 ```sh
-docker pull ruanad/htrfit:v2.0.0
-docker run -it --rm ruanad/htrfit:v2.0.0
+docker pull ruanad/htrfit:v2.1
+docker run -it --rm ruanad/htrfit:v2.1
 ```
 
 ## Biosphere virtual machine