old mode 100755

new mode 100644

@@ -24,6 +24,7 @@ reference:

   - plotDimReduceCluster

   - plotDimReduceFeature

   - plotDimReduceModule

+  - plotDimReduceGrid  

   - plotCeldaViolin  

   - celdaHeatmap

@@ -34,7 +35,6 @@ reference:

   - plotDecontXContamination

   - plotDecontXMarkerExpression

   - plotDecontXMarkerPercentage

-

   - decontXcounts

 - title: Functions for determining the numbers of clusters in celda

@@ -46,13 +46,13 @@ reference:

   - celdaGridSearch

   - plotGridSearchPerplexity

   - perplexity

-  - celdaPerplexity  

   - resamplePerplexity

   - selectBestModel

   - resList  

   - subsetCeldaList  

   - appendCeldaList

-

+  - celdaPerplexity

+  

 - title: Miscellaneous celda functions 

   desc: Various functions for manipulation of celda results

   contents:

@@ -97,7 +97,29 @@ reference:

   - sampleCells

   - contaminationSim

-

+- title: internal

+  contents:

+  - availableModels

+  - celdaCGMod

+  - celdaCGSim 

+  - celdaCMod

+  - celdaCSim

+  - celdaGMod

+  - celdaGSim

+  - celdaModel

+  - celdatosce

+  - compareCountMatrix

+  - countChecksum

+  - eigenMatMultInt

+  - eigenMatMultNumeric

+  - fastNormProp

+  - fastNormPropLog

+  - fastNormPropSqrt

+  - nonzero

+  - semiPheatmap

+  - '`celdaPerplexity,celdaList-method`'

+  - '`countChecksum,celdaList-method`'

+  

 navbar:

   title: "celda"

   left:

@@ -34,6 +34,7 @@ reference:

   - plotDecontXContamination

   - plotDecontXMarkerExpression

   - plotDecontXMarkerPercentage

+

   - decontXcounts

 - title: Functions for determining the numbers of clusters in celda

@@ -101,7 +102,7 @@ navbar:

   title: "celda"

   left:

     - icon: fa-home fa-lg

-      href: http://celda.camplab.net/

+      href: https://www.camplab.net/celda

     - text: "Installation"

       href: articles/articles/installation.html

     - text: "Vignettes"

@@ -101,7 +101,7 @@ navbar:

   title: "celda"

   left:

     - icon: fa-home fa-lg

-      href: index.html

+      href: http://celda.camplab.net/

     - text: "Installation"

       href: articles/articles/installation.html

     - text: "Vignettes"

@@ -106,11 +106,13 @@ navbar:

       href: articles/articles/installation.html

     - text: "Vignettes"

       menu:

-      - text: "Analysis of PBMC3K with Celda"

+      - text: "Celda - Analysis of PBMC3K"

         href: articles/articles/celda_pbmc3k.html

-      - text: "Decontamination of PBMC4K with DecontX"

+      - text: "DecontX - Decontamination of PBMC4K"

         href: articles/articles/decontX_pbmc4k.html

     - text: "Reference"

       href: reference/index.html

+    - text: "News"

+      href: news/index.html

     - icon: fa-github

       href: https://github.com/campbio/celda

@@ -3,106 +3,114 @@ template:

     bootswatch: yeti

 reference:

-- title: Function Documentation

-  desc: Man pages for all functions exported by celda

+- title: Primary celda functions

+  desc: Functions for clustering of cells

   contents:

-  - '`available_models`'

-  - '`calc.perplexity`'

-  - '`calc.perplexity2`'

-  - '`calculateLoglikFromVariables.celda_C`'

-  - '`calculateLoglikFromVariables.celda_CG`'

-  - '`calculateLoglikFromVariables.celda_G`'

-  - '`calculateLoglikFromVariables`'

-  - '`calculatePerplexity.celda_C`'

-  - '`calculatePerplexity.celda_CG`'

-  - '`calculatePerplexity.celda_G`'

-  - '`calculatePerplexity`'

-  - '`calculatePerplexityWithResampling`'

-  - '`calculateTsne`'

-  - '`cC.decomposeCounts`'

-  - '`cCG.decomposeCounts`'

-  - '`celda`'

-  - '`celdaGridSearch`'

-  - '`celdaHeatmap.celda_C`'

-  - '`celdaHeatmap.celda_CG`'

-  - '`celdaHeatmap.celda_G`'

-  - '`celdaHeatmap`'

-  - '`celdaProbabilityMap.celda_C`'

-  - '`celdaProbabilityMap.celda_CG`'

-  - '`celdaProbabilityMap`'

-  - '`celdaTsne.celda_C`'

-  - '`celdaTsne.celda_CG`'

-  - '`celdaTsne.celda_G`'

-  - '`celdaTsne`'

-  - '`celda_C`'

-  - '`celda_CG`'

-  - '`celda_G`'

-  - '`cG.decomposeCounts`'

-  - '`clusterProbability.celda_C`'

-  - '`clusterProbability.celda_CG`'

-  - '`clusterProbability.celda_G`'

-  - '`clusterProbability`'

-  - '`compareCountMatrix`'

-  - '`completeLogLikelihood`'

-  - '`distinct_colors`'

-  - '`eigenMatMultInt`'

-  - '`factorizeMatrix.celda_C`'

-  - '`factorizeMatrix.celda_CG`'

-  - '`factorizeMatrix.celda_G`'

-  - '`factorizeMatrix`'

-  - '`fastNormProp`'

-  - '`fastNormPropLog`'

-  - '`fastNormPropSqrt`'

-  - '`featureModuleLookup.celda_C`'

-  - '`featureModuleLookup.celda_CG`'

-  - '`featureModuleLookup.celda_G`'

-  - '`featureModuleLookup`'

-  - '`finalLogLikelihood`'

-  - '`moduleHeatmap`'

-  - '`normalizeCounts`'

-  - '`pbmc_res`'

-  - '`pbmc_select`'

-  - '`plotDimReduceCluster`'

-  - '`plotDimReduceGene`'

-  - '`plotDimReduceGrid`'

-  - '`plotDimReduceState`'

-  - '`plotGridSearchPerplexity.celda_C`'

-  - '`plotGridSearchPerplexity.celda_CG`'

-  - '`plotGridSearchPerplexity.celda_G`'

-  - '`plotGridSearchPerplexity`'

-  - '`plotHeatmap`'

-  - '`recodeClusterY`'

-  - '`recodeClusterZ`'

-  - '`runParams`'

-  - '`sample.cells`'

-  - '`selectBestModel`'

-  - '`semi_pheatmap`'

-  - '`simulateCells.celda_C`'

-  - '`simulateCells.celda_CG`'

-  - '`simulateCells.celda_G`'

-  - '`simulateCells`'

-  - '`subsetCeldaList`'

-  - '`topRank`'

+  - celda_CG

+  - celda_C

+  - celda_G

+  - reportCeldaCGRun

+  - reportCeldaCGPlotResults

+  - selectFeatures  

+  - splitModule

+

+- title: Visualization functions for celda results

+  desc: Functions for displaying celda resuls on 2-D embeddings, heatmaps, and violin plots

+  contents:

+  - celdaUmap

+  - celdaTsne

+  - moduleHeatmap

+  - celdaProbabilityMap

+  - plotDimReduceCluster

+  - plotDimReduceFeature

+  - plotDimReduceModule

+  - plotCeldaViolin  

+  - celdaHeatmap

+

+- title: Primary decontX functions

+  desc: Functions for estimating and displaying contamination with decontX

+  contents:

+  - decontX

+  - plotDecontXContamination

+  - plotDecontXMarkerExpression

+  - plotDecontXMarkerPercentage

+  - decontXcounts

+  

+- title: Functions for determining the numbers of clusters in celda

+  desc: Functions for running and comparing multiple celda models with different number of modules or cell populations

+  contents:

+  - recursiveSplitCell

+  - recursiveSplitModule

+  - plotRPC

+  - celdaGridSearch

+  - plotGridSearchPerplexity

+  - perplexity

+  - celdaPerplexity  

+  - resamplePerplexity

+  - selectBestModel

+  - resList  

+  - subsetCeldaList  

+  - appendCeldaList

+

+- title: Miscellaneous celda functions 

+  desc: Various functions for manipulation of celda results

+  contents:

+  - celdaClusters

+  - celdaModules

+  - recodeClusterY

+  - recodeClusterZ

+  - reorderCelda  

+  - featureModuleLookup

+  - featureModuleTable

+  - celda

+  - params  

+  - runParams  

+  - factorizeMatrix

+  - bestLogLikelihood

+  - clusterProbability

+  - geneSetEnrich

+  - plotHeatmap

+  - retrieveFeatureIndex

+  - normalizeCounts

+  - distinctColors

+  - matrixNames

+  - logLikelihood

+  - logLikelihoodHistory

+  - topRank

+  - sampleLabel

+

+- title: Simulation functions

+  desc: Functions for generating data from the generative process of each model 

+  contents:

+  - simulateCells

+  - simulateContamination

+

+- title: Data objects

+  desc: Small data objects used in examples

+  contents:

+  - sceCeldaCG

+  - sceCeldaC

+  - sceCeldaG

+  - sceCeldaCGGridSearch

+  - celdaCGGridSearchRes

+  - sampleCells

+  - contaminationSim

+

 navbar:

-  structure:

-    left:

-    - home

-    - intro

-    - reference

-    - articles

-    - tutorials

-    - news

-    right: github

-  components:

-    home:

-      icon: fa-home fa-lg

+  title: "celda"

+  left:

+    - icon: fa-home fa-lg

       href: index.html

-    reference:

-      text: Reference

-      href: reference/index.html

-    articles:

-      text: Articles

+    - text: "Installation"

+      href: articles/articles/installation.html

+    - text: "Vignettes"

       menu:

-      - text: Analyzing single-cell RNA-seq count data with Celda

-        href: articles/celda-analysis.html

+      - text: "Analysis of PBMC3K with Celda"

+        href: articles/articles/celda_pbmc3k.html

+      - text: "Decontamination of PBMC4K with DecontX"

+        href: articles/articles/decontX_pbmc4k.html

+    - text: "Reference"

+      href: reference/index.html

+    - icon: fa-github

+      href: https://github.com/campbio/celda

@@ -44,7 +44,6 @@ reference:

   - '`clusterProbability`'

   - '`compareCountMatrix`'

   - '`completeLogLikelihood`'

-  - '`differentialExpression`'

   - '`distinct_colors`'

   - '`eigenMatMultInt`'

   - '`factorizeMatrix.celda_C`'

new file mode 100755

@@ -0,0 +1,109 @@

+template:

+  params:

+    bootswatch: yeti

+

+reference:

+- title: Function Documentation

+  desc: Man pages for all functions exported by celda

+  contents:

+  - '`available_models`'

+  - '`calc.perplexity`'

+  - '`calc.perplexity2`'

+  - '`calculateLoglikFromVariables.celda_C`'

+  - '`calculateLoglikFromVariables.celda_CG`'

+  - '`calculateLoglikFromVariables.celda_G`'

+  - '`calculateLoglikFromVariables`'

+  - '`calculatePerplexity.celda_C`'

+  - '`calculatePerplexity.celda_CG`'

+  - '`calculatePerplexity.celda_G`'

+  - '`calculatePerplexity`'

+  - '`calculatePerplexityWithResampling`'

+  - '`calculateTsne`'

+  - '`cC.decomposeCounts`'

+  - '`cCG.decomposeCounts`'

+  - '`celda`'

+  - '`celdaGridSearch`'

+  - '`celdaHeatmap.celda_C`'

+  - '`celdaHeatmap.celda_CG`'

+  - '`celdaHeatmap.celda_G`'

+  - '`celdaHeatmap`'

+  - '`celdaProbabilityMap.celda_C`'

+  - '`celdaProbabilityMap.celda_CG`'

+  - '`celdaProbabilityMap`'

+  - '`celdaTsne.celda_C`'

+  - '`celdaTsne.celda_CG`'

+  - '`celdaTsne.celda_G`'

+  - '`celdaTsne`'

+  - '`celda_C`'

+  - '`celda_CG`'

+  - '`celda_G`'

+  - '`cG.decomposeCounts`'

+  - '`clusterProbability.celda_C`'

+  - '`clusterProbability.celda_CG`'

+  - '`clusterProbability.celda_G`'

+  - '`clusterProbability`'

+  - '`compareCountMatrix`'

+  - '`completeLogLikelihood`'

+  - '`differentialExpression`'

+  - '`distinct_colors`'

+  - '`eigenMatMultInt`'

+  - '`factorizeMatrix.celda_C`'

+  - '`factorizeMatrix.celda_CG`'

+  - '`factorizeMatrix.celda_G`'

+  - '`factorizeMatrix`'

+  - '`fastNormProp`'

+  - '`fastNormPropLog`'

+  - '`fastNormPropSqrt`'

+  - '`featureModuleLookup.celda_C`'

+  - '`featureModuleLookup.celda_CG`'

+  - '`featureModuleLookup.celda_G`'

+  - '`featureModuleLookup`'

+  - '`finalLogLikelihood`'

+  - '`moduleHeatmap`'

+  - '`normalizeCounts`'

+  - '`pbmc_res`'

+  - '`pbmc_select`'

+  - '`plotDimReduceCluster`'

+  - '`plotDimReduceGene`'

+  - '`plotDimReduceGrid`'

+  - '`plotDimReduceState`'

+  - '`plotGridSearchPerplexity.celda_C`'

+  - '`plotGridSearchPerplexity.celda_CG`'

+  - '`plotGridSearchPerplexity.celda_G`'

+  - '`plotGridSearchPerplexity`'

+  - '`plotHeatmap`'

+  - '`recodeClusterY`'

+  - '`recodeClusterZ`'

+  - '`runParams`'

+  - '`sample.cells`'

+  - '`selectBestModel`'

+  - '`semi_pheatmap`'

+  - '`simulateCells.celda_C`'

+  - '`simulateCells.celda_CG`'

+  - '`simulateCells.celda_G`'

+  - '`simulateCells`'

+  - '`subsetCeldaList`'

+  - '`topRank`'

+

+navbar:

+  structure:

+    left:

+    - home

+    - intro

+    - reference

+    - articles

+    - tutorials

+    - news

+    right: github

+  components:

+    home:

+      icon: fa-home fa-lg

+      href: index.html

+    reference:

+      text: Reference

+      href: reference/index.html

+    articles:

+      text: Articles

+      menu:

+      - text: Analyzing single-cell RNA-seq count data with Celda

+        href: articles/celda-analysis.html