From 497545a7307980beafcd51510a912c8a0b6d688a Mon Sep 17 00:00:00 2001 From: danro9685 Date: Mon, 22 Jul 2024 08:06:02 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Batzoglo?= =?UTF-8?q?uLabSU/SIMLR@47546693715b170009e45ae2f65253668e4fa97c=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 14 ++-- LICENSE-text.html | 16 ++--- LICENSE.html | 14 ++-- articles/index.html | 14 ++-- articles/v1_introduction.html | 23 +++---- articles/v2_running_SIMLR.html | 19 +++--- authors.html | 24 +++---- index.html | 14 ++-- pkgdown.yml | 9 ++- reference/BuettnerFlorian.html | 30 ++++----- reference/SIMLR.html | 34 +++++----- .../SIMLR_Estimate_Number_of_Clusters.html | 24 +++---- reference/SIMLR_Feature_Ranking.html | 28 ++++---- reference/SIMLR_Large_Scale.html | 34 +++++----- reference/ZeiselAmit.html | 30 ++++----- reference/index.html | 14 ++-- sitemap.xml | 64 +++++-------------- 17 files changed, 181 insertions(+), 224 deletions(-) diff --git a/404.html b/404.html index 1005b00..7d8965d 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -100,16 +100,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/LICENSE-text.html b/LICENSE-text.html index 04ec32b..66d9487 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -3,7 +3,7 @@ - +
- +
@@ -729,7 +729,7 @@

License

may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read -<http://www.gnu.org/philosophy/why-not-lgpl.html>. +<http://www.gnu.org/philosophy/why-not-lgpl.html>.
@@ -747,15 +747,15 @@

License

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/LICENSE.html b/LICENSE.html index 331bffb..97d96ba 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -3,7 +3,7 @@ - +
- +
@@ -329,15 +329,15 @@

How to Apply These Terms

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/articles/index.html b/articles/index.html index 3370a11..c2821e6 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,7 +3,7 @@ - +
- +
@@ -74,15 +74,15 @@

All vignettes

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/articles/v1_introduction.html b/articles/v1_introduction.html index 756280d..fc26117 100644 --- a/articles/v1_introduction.html +++ b/articles/v1_introduction.html @@ -12,14 +12,13 @@ - - +
- +
@@ -87,9 +86,9 @@

Luca De

Serafim Batzoglou

-

May 07, 2024

+

July 22, 2024

- Source: vignettes/v1_introduction.Rmd + Source: vignettes/v1_introduction.Rmd
@@ -143,9 +142,7 @@

Debug +

@@ -158,16 +155,16 @@

Debug

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/articles/v2_running_SIMLR.html b/articles/v2_running_SIMLR.html index bd174a8..f1ab758 100644 --- a/articles/v2_running_SIMLR.html +++ b/articles/v2_running_SIMLR.html @@ -12,14 +12,13 @@ - - +
- +
@@ -87,9 +86,9 @@

Luca De

Serafim Batzoglou

-

May 07, 2024

+

July 22, 2024

- Source: vignettes/v2_running_SIMLR.Rmd + Source: vignettes/v2_running_SIMLR.Rmd
@@ -680,16 +679,16 @@

May 07, 2024

-

Site built with pkgdown 2.0.9.9000.

+

Site built with pkgdown 2.1.0.9000.

- - + + diff --git a/authors.html b/authors.html index e145a32..afae16e 100644 --- a/authors.html +++ b/authors.html @@ -3,7 +3,7 @@ - +
- +
@@ -57,13 +57,13 @@

Authors and Citation

- +

  • Daniele Ramazzotti. Author.

  • -

    Bo Wang. Author. +

    Bo Wang. Author.

  • @@ -71,21 +71,21 @@

    Authors and Citation

  • -

    Serafim Batzoglou. Contributor. +

    Serafim Batzoglou. Contributor.

Citation

- Source: DESCRIPTION + Source: DESCRIPTION

Ramazzotti D, Wang B, De Sano L (2024). SIMLR: Single-cell Interpretation via Multi-kernel LeaRning (SIMLR). -R package version 1.30.0, https://github.com/BatzoglouLabSU/SIMLR. +R package version 1.30.0, https://github.com/BatzoglouLabSU/SIMLR. 

@Manual{,
   title = {SIMLR: Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)},
@@ -106,15 +106,15 @@ 
Citation

 
 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/index.html b/index.html
index 26b02fd..666e8bc 100644
--- a/index.html
+++ b/index.html
@@ -19,7 +19,7 @@
 
 
 
-    
+
 
     

       

 
 
-      
+
 
       

   

@@ -202,16 +202,16 @@ 
Developers

 
 

   

-
Site built with pkgdown 2.0.9.9000.

+
Site built with pkgdown 2.1.0.9000.

 

 
       
 

 
-  
 
 
-  
+
+
 
   
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 801abf2..538802f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,8 +1,7 @@
-pandoc: 3.1.13
-pkgdown: 2.0.9.9000
-pkgdown_sha: 7bc81933fa3e63252a109010ecf361f109a6744c
+pandoc: '3.2'
+pkgdown: 2.1.0.9000
+pkgdown_sha: 2841c0f994fda7f7c7da94034bd24e3882fc7a37
 articles:
   v1_introduction: v1_introduction.html
   v2_running_SIMLR: v2_running_SIMLR.html
-last_built: 2024-05-07T16:33Z
-
+last_built: 2024-07-22T08:04Z
diff --git a/reference/BuettnerFlorian.html b/reference/BuettnerFlorian.html
index 046f583..77dc6b2 100644
--- a/reference/BuettnerFlorian.html
+++ b/reference/BuettnerFlorian.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
test dataset for SIMLR

-    Source: R/data.R
+    Source: R/data.R
     
     

 
@@ -76,14 +76,12 @@ 
Source

     

     

     
Value

-    
-
-
list of 6: 
-	in_X = input dataset as an (m x n) gene expression measurements of individual cells, 
- 	n_clust = number of clusters (number of distinct true labels), 
- 	true_labs = ground true of cluster assignments for each of the n_clust clusters, 
- 	seed = seed used to compute the results for the example, 
- 	results = result by SIMLR for the inputs defined as described, 
+    
list of 6:
+	in_X = input dataset as an (m x n) gene expression measurements of individual cells,
+ 	n_clust = number of clusters (number of distinct true labels),
+ 	true_labs = ground true of cluster assignments for each of the n_clust clusters,
+ 	seed = seed used to compute the results for the example,
+ 	results = result by SIMLR for the inputs defined as described,
  	nmi = normalized mutual information as a measure of the inferred clusters compared to the true labels

     

 
@@ -99,15 +97,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/SIMLR.html b/reference/SIMLR.html
index ce27c89..df4ff17 100644
--- a/reference/SIMLR.html
+++ b/reference/SIMLR.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
SIMLR

-    Source: R/SIMLR.R
+    Source: R/SIMLR.R
     
     

 
@@ -76,7 +76,9 @@ 
SIMLR

 
     

     
Arguments

-    
X

+
+
+
X

 
an (m x n) data matrix of gene expression measurements of individual cells or
 and object of class SCESet

 
@@ -107,15 +109,11 @@ 
Arguments

 

     

     
Value

-    
-
-
clusters the cells based on SIMLR and their similarities

-
-
-
list of 8 elements describing the clusters obtained by SIMLR, of which y are the resulting clusters: 
+    
clusters the cells based on SIMLR and their similarities

+
list of 8 elements describing the clusters obtained by SIMLR, of which y are the resulting clusters:
 	y = results of k-means clusterings,
- 	S = similarities computed by SIMLR, 
- 	F = results from network diffiusion, 
+ 	S = similarities computed by SIMLR,
+ 	F = results from network diffiusion,
  	ydata = data referring the the results by k-means,
  	alphaK = clustering coefficients,
  	execution.time = execution time of the present run,
@@ -7347,7 +7345,7 @@ 
Examples

 #> 
 #> $execution.time
 #>    user  system elapsed 
-#>   8.849   4.451   9.414 
+#>   9.157   4.513   9.809 
 #> 
 #> $converge
 #>  [1] 0.3728507 0.2757306 0.2576427 0.2520954 0.2483652 0.2446142 0.2391406
@@ -7553,15 +7551,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/SIMLR_Estimate_Number_of_Clusters.html b/reference/SIMLR_Estimate_Number_of_Clusters.html
index da52dd1..fe434af 100644
--- a/reference/SIMLR_Estimate_Number_of_Clusters.html
+++ b/reference/SIMLR_Estimate_Number_of_Clusters.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
SIMLR Estimate Number of Clusters

-    Source: R/SIMLR_Estimate_Number_of_Clusters.R
+    Source: R/SIMLR_Estimate_Number_of_Clusters.R
     
     

 
@@ -68,7 +68,9 @@ 
SIMLR Estimate Number of Clusters

 
     

     
Arguments

-    
X

+
+
+
X

 
an (m x n) data matrix of gene expression measurements of individual cells

 
 
@@ -82,9 +84,7 @@ 
Arguments

 

     

     
Value

-    
-
-
a list of 2 elements: K1 and K2 with an estimation of the best clusters (the lower 
+    
a list of 2 elements: K1 and K2 with an estimation of the best clusters (the lower
 values the better) as discussed in the original paper of SIMLR

     

 
@@ -115,15 +115,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/SIMLR_Feature_Ranking.html b/reference/SIMLR_Feature_Ranking.html
index 043f4e5..ca33f49 100644
--- a/reference/SIMLR_Feature_Ranking.html
+++ b/reference/SIMLR_Feature_Ranking.html
@@ -1,10 +1,10 @@
 
-SIMLR Feature Ranking — SIMLR_Feature_Ranking • SIMLRSIMLR Feature Ranking — SIMLR_Feature_Ranking • SIMLR
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
SIMLR Feature Ranking

-    Source: R/SIMLR_Feature_Ranking.R
+    Source: R/SIMLR_Feature_Ranking.R
     
     

 
     

-    
perform the SIMLR feature ranking algorithm. This takes as input the original 
+    
perform the SIMLR feature ranking algorithm. This takes as input the original
 input data and the corresponding similarity matrix computed by SIMLR

     

 
@@ -70,7 +70,9 @@ 
SIMLR Feature Ranking

 
     

     
Arguments

-    
A

+
+
+
A

 
an (n x n) similarity matrix by SIMLR

 
 
@@ -80,9 +82,7 @@ 
Arguments

 

     

     
Value

-    
-
-
a list of 2 elements: pvalues and ranking ordering over the n covariates 
+    
a list of 2 elements: pvalues and ranking ordering over the n covariates
 as estimated by the method

     

 
@@ -2650,15 +2650,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/SIMLR_Large_Scale.html b/reference/SIMLR_Large_Scale.html
index 8a450db..018f589 100644
--- a/reference/SIMLR_Large_Scale.html
+++ b/reference/SIMLR_Large_Scale.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

     

     
SIMLR Large Scale

-    Source: R/SIMLR_Large_Scale.R
+    Source: R/SIMLR_Large_Scale.R
     
     

 
@@ -68,7 +68,9 @@ 
SIMLR Large Scale

 
     

     
Arguments

-    
X

+
+
+
X

 
an (m x n) data matrix of gene expression measurements of individual cells or
 and object of class SCESet

 
@@ -95,15 +97,11 @@ 
Arguments

 

     

     
Value

-    
-
-
clusters the cells based on SIMLR Large Scale and their similarities

-
-
-
list of 8 elements describing the clusters obtained by SIMLR, of which y are the resulting clusters: 
+    
clusters the cells based on SIMLR Large Scale and their similarities

+
list of 8 elements describing the clusters obtained by SIMLR, of which y are the resulting clusters:
 	y = results of k-means clusterings,
- 	S0 = similarities computed by SIMLR, 
- 	F = results from the large scale iterative procedure, 
+ 	S0 = similarities computed by SIMLR,
+ 	F = results from the large scale iterative procedure,
  	ydata = data referring the the results by k-means,
  	alphaK = clustering coefficients,
  	val = distances from the k-nearest neighbour search,
@@ -2865,7 +2863,7 @@ 
Examples

 #> 
 #> $execution.time
 #>    user  system elapsed 
-#>   0.433   0.506   0.344 
+#>   0.474   0.470   0.343 
 #> 
 # }
 
@@ -2883,15 +2881,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/ZeiselAmit.html b/reference/ZeiselAmit.html
index 84ff746..a14e9ca 100644
--- a/reference/ZeiselAmit.html
+++ b/reference/ZeiselAmit.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 

 
-      
+
 
       

   

     

     
test dataset for SIMLR large scale

-    Source: R/data.R
+    Source: R/data.R
     
     

 
@@ -76,14 +76,12 @@ 
Source

     

     

     
Value

-    
-
-
list of 6: 
-	in_X = input dataset as an (m x n) gene expression measurements of individual cells, 
- 	n_clust = number of clusters (number of distinct true labels), 
- 	true_labs = ground true of cluster assignments for each of the n_clust clusters, 
- 	seed = seed used to compute the results for the example, 
- 	results = result by SIMLR for the inputs defined as described, 
+    
list of 6:
+	in_X = input dataset as an (m x n) gene expression measurements of individual cells,
+ 	n_clust = number of clusters (number of distinct true labels),
+ 	true_labs = ground true of cluster assignments for each of the n_clust clusters,
+ 	seed = seed used to compute the results for the example,
+ 	results = result by SIMLR for the inputs defined as described,
  	nmi = normalized mutual information as a measure of the inferred clusters compared to the true labels

     

 
@@ -99,15 +97,15 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/index.html b/reference/index.html
index 57d64a5..cc96287 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -3,7 +3,7 @@
 
 
 
-    
+
 
     

       

   

 
 
-      
+
 
       

   

@@ -97,15 +97,15 @@ 
All functions 
 
 

-  
Site built with pkgdown 2.0.9.9000.

+  
Site built with pkgdown 2.1.0.9000.

 

 
       

 
-  
 
 
-  
+
+
 
   
 
diff --git a/sitemap.xml b/sitemap.xml
index 1929748..0fec622 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -1,48 +1,18 @@
-
-
-  
-    /404.html
-  
-  
-    /LICENSE-text.html
-  
-  
-    /LICENSE.html
-  
-  
-    /articles/index.html
-  
-  
-    /articles/v1_introduction.html
-  
-  
-    /articles/v2_running_SIMLR.html
-  
-  
-    /authors.html
-  
-  
-    /index.html
-  
-  
-    /reference/BuettnerFlorian.html
-  
-  
-    /reference/SIMLR.html
-  
-  
-    /reference/SIMLR_Estimate_Number_of_Clusters.html
-  
-  
-    /reference/SIMLR_Feature_Ranking.html
-  
-  
-    /reference/SIMLR_Large_Scale.html
-  
-  
-    /reference/ZeiselAmit.html
-  
-  
-    /reference/index.html
-  
+
+/404.html
+/LICENSE-text.html
+/LICENSE.html
+/articles/index.html
+/articles/v1_introduction.html
+/articles/v2_running_SIMLR.html
+/authors.html
+/index.html
+/reference/BuettnerFlorian.html
+/reference/SIMLR.html
+/reference/SIMLR_Estimate_Number_of_Clusters.html
+/reference/SIMLR_Feature_Ranking.html
+/reference/SIMLR_Large_Scale.html
+/reference/ZeiselAmit.html
+/reference/index.html
 
+