Update readme and news

NEWS.md

@@ -1,7 +1,7 @@
 # News
 All notable changes will be documented in this file.
 
-## [0.3] - 2020-09-16
+## [0.3] - 2020-09-19
 ### Added
 - Add support for `glmGamPoi` as method to estimate the model parameters; thanks @yuhanH for his pull request
 - Add option to use `theta.md`, `theta.mm` or`theta.ml` to estimate theta when `method = 'poisson'`

README.md

@@ -7,15 +7,22 @@ This package was developed by Christoph Hafemeister in [Rahul Satija's lab](http
 `devtools::install_github(repo = 'ChristophH/sctransform')`  
 `normalized_data <- sctransform::vst(umi_count_matrix)$y`
 
+(you can also install from CRAN: `install.packages('sctransform'))`)
+
 ## Help
 For usage examples see vignettes in inst/doc or use the built-in help after installation  
 `?sctransform::vst`  
 
 Available vignettes:  
-[Variance stabilizing transformation](https://rawgit.com/ChristophH/sctransform/master/inst/doc/variance_stabilizing_transformation.html)  
-[Using sctransform in Seurat](https://rawgit.com/ChristophH/sctransform/master/inst/doc/seurat.html)  
+[Variance stabilizing transformation](https://rawgit.com/ChristophH/sctransform/develop/supplement/variance_stabilizing_transformation.html)  
+[Using sctransform in Seurat](https://rawgit.com/ChristophH/sctransform/develop/supplement/seurat.html)  
 
 ## News
+The latest version of `sctransform` now supports the [glmGamPoi](https://github.com/const-ae/glmGamPoi) package to speed up the model fitting step. You can see more about the different methods supported and how they compare in terms of results and speed [in this new vignette](https://rawgit.com/ChristophH/sctransform/develop/supplement/method_comparison.html).
+
+Also note that default theta regularization is now based on overdispersion factor (`1 + m / theta` where m is the geometric mean of the observed counts) not `log10(theta)`. The old behavior is still available via `theta_regularization` parameter. You can see how this changes (or doesn't change) the results [in this new vignette](https://rawgit.com/ChristophH/sctransform/develop/supplement/theta_regularization.html).
+
+For a detailed change log have a look at the file [NEWS.md](https://github.com/ChristophH/sctransform/blob/develop/NEWS.md)
 
 
 ## Reference