update vignette and readme

SydneyBioX · Nov 28, 2023 · c16c549 · c16c549
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diff --git a/README.md b/README.md
@@ -24,20 +24,8 @@ devtools::install_github("SydneyBioX/scFeatures")
 
 ##  Vignettes
 
-A number of vignettes are provided in the Vignettes folder of this repo. These can also be viewed here by clicking the link below.  
-
-### Feaeture generation using scFeatures
-
-* [Brief vignette](https://sydneybiox.github.io/scFeatures/articles/scFeatures_summary.html) - The brief vignette is a quick starting point and provides a checklist of the functions to apply on single-cell and spatial data.   
-* [Detailed vignette with case studies](https://sydneybiox.github.io/scFeatures/articles/scFeatures_detail.html) - This provides an in-depth description for each feature types and explanation of the output. It contains a step-by-step case study to the application of scFeatures on i) scRNA-seq data, ii) spatial proteomics data and iii) spatial transcriptomics data.    
-
-
-### Association study of the features with conditions
-
-We provide a function `run_association_study_report(scfeatures_result, output_folder)` that automatically runs association study and generates an html output report. The report visualises the features most associated with conditions (eg, diseased vs non-diseased).   
-
-*  [Association study vignette](https://sydneybiox.github.io/scFeatures/articles/scFeatures_associationstudy.html) - This explains the usage of the function.
-
+Please see https://sydneybiox.github.io/scFeatures/articles/scFeatures_overview.html.     
+
 ## Reference
 
 Cao, Y., Lin, Y., Patrick, E., Yang, P., & Yang, J. Y. H. (2022). scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction. In O. Vitek (Ed.), Bioinformatics (Vol. 38, Issue 20, pp. 4745–4753). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btac590 
diff --git a/docs/articles/scFeatures_overview.html b/docs/articles/scFeatures_overview.html
diff --git a/docs/articles/scFeatures_overview_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/scFeatures_overview_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/scFeatures_overview_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/scFeatures_overview_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,9 +1,9 @@
-pandoc: 3.1.2
+pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   scFeatures_overview: scFeatures_overview.html
-last_built: 2023-10-04T03:06Z
+last_built: 2023-11-28T09:11Z
 urls:
   reference: https://sydneybiox.github.io/scFeatures/reference
   article: https://sydneybiox.github.io/scFeatures/articles

diff --git a/docs/reference/get_num_cell_per_spot.html b/docs/reference/get_num_cell_per_spot.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/remove_mito_ribo.html b/docs/reference/remove_mito_ribo.html
diff --git a/docs/reference/run_CCI.html b/docs/reference/run_CCI.html
diff --git a/docs/reference/run_L_function.html b/docs/reference/run_L_function.html