From 489c7d5285089ac84f432eb9eeb0150815058f38 Mon Sep 17 00:00:00 2001 From: zktuong Date: Sat, 8 Feb 2025 02:50:11 +0000 Subject: [PATCH] Built site for dandelionR@0.99.9: 121379f --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/dandelionR.html | 7 ++----- articles/index.html | 2 +- articles/vignette_reproduce_original.html | 7 ++----- authors.html | 2 +- index.html | 2 +- news/index.html | 6 +++--- pkgdown.yml | 2 +- reference/chainAssign.html | 2 +- reference/dandelionR.html | 2 +- reference/demo_airr.html | 2 +- reference/demo_sce.html | 2 +- reference/differentiationProbabilities.html | 2 +- reference/dot-KNNind.html | 2 +- reference/dot-addColData.html | 2 +- reference/dot-allowedChain.html | 2 +- reference/dot-calDif.html | 2 +- reference/dot-classCheck.html | 2 +- reference/dot-collapse_nested_list.html | 2 +- reference/dot-constructMarkovChain.html | 2 +- reference/dot-determExtractColN.html | 2 +- reference/dot-determTerminal.html | 2 +- reference/dot-determineMultiscaleSpace.html | 2 +- reference/dot-extractVdj.html | 2 +- reference/dot-featureSpaceConstruct.html | 2 +- reference/dot-filterCells.html | 2 +- reference/dot-filterProductivity.html | 2 +- reference/dot-filterUnmapped.html | 2 +- reference/dot-findNewWaypoints.html | 2 +- reference/dot-generateExtractColumn.html | 2 +- reference/dot-generateExtractName.html | 2 +- reference/dot-getPbs.html | 2 +- reference/dot-getPbsCol.html | 2 +- reference/dot-getPbsPerCol.html | 2 +- reference/dot-maxMinSampling.html | 2 +- reference/dot-minMaxScale.html | 2 +- reference/dot-normalizeFeatureSpace.html | 2 +- reference/dot-normalizePerVDJ.html | 2 +- reference/dot-packFeatureSpace.html | 2 +- reference/dot-removeEdge.html | 2 +- reference/dot-subsetSce.html | 2 +- reference/dot-terminalStateFromMarkovChain.html | 2 +- reference/dot-typeCheck.html | 2 +- reference/dot-waypiontsPerCol.html | 2 +- reference/formatVdj.html | 2 +- reference/index.html | 2 +- reference/markovProbability.html | 2 +- reference/miloUmap.html | 2 +- reference/projectProbability.html | 2 +- reference/projectPseudotimeToCell.html | 2 +- reference/sce_vdj.html | 2 +- reference/setupVdjPseudobulk.html | 2 +- reference/splitCTgene.html | 2 +- reference/vdjPseudobulk.html | 2 +- 55 files changed, 59 insertions(+), 65 deletions(-) diff --git a/404.html b/404.html index f848499..4b14c0c 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/LICENSE-text.html b/LICENSE-text.html index 55566ba..f7105dc 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/articles/dandelionR.html b/articles/dandelionR.html index 0e7d451..4c21ec5 100644 --- a/articles/dandelionR.html +++ b/articles/dandelionR.html @@ -32,7 +32,7 @@ dandelionR - 0.99.8 + 0.99.9 @@ -74,9 +74,6 @@

Starting From scRepertoire

-

Jiawei Yu

-

Kelvin -Tuong

2025-02-08

@@ -592,7 +589,7 @@

Session info## [13] S4Vectors_0.45.2 BiocGenerics_0.53.6 ## [15] generics_0.1.3 MatrixGenerics_1.19.1 ## [17] matrixStats_1.5.0 scRepertoire_2.3.2 -## [19] ggplot2_3.5.1 dandelionR_0.99.8 +## [19] ggplot2_3.5.1 dandelionR_0.99.9 ## [21] BiocStyle_2.35.0 ## ## loaded via a namespace (and not attached): diff --git a/articles/index.html b/articles/index.html index 5ded22c..4b80d6d 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9

diff --git a/articles/vignette_reproduce_original.html b/articles/vignette_reproduce_original.html index 5581369..2055999 100644 --- a/articles/vignette_reproduce_original.html +++ b/articles/vignette_reproduce_original.html @@ -32,7 +32,7 @@ dandelionR - 0.99.8 + 0.99.9
@@ -75,9 +75,6 @@

Reproducing the original dandelion method/paper

-

Jiawei Yu

-

Kelvin -Tuong

2025-02-08

@@ -342,7 +339,7 @@

Session info## [13] S4Vectors_0.45.2 BiocGenerics_0.53.6 ## [15] generics_0.1.3 MatrixGenerics_1.19.1 ## [17] matrixStats_1.5.0 scRepertoire_2.3.2 -## [19] ggplot2_3.5.1 dandelionR_0.99.8 +## [19] ggplot2_3.5.1 dandelionR_0.99.9 ## [21] BiocStyle_2.35.0 ## ## loaded via a namespace (and not attached): diff --git a/authors.html b/authors.html index 842c54b..1d71458 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9

diff --git a/index.html b/index.html index 30b0e9e..67a5877 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/news/index.html b/news/index.html index dfc1e74..32195b8 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 @@ -55,11 +55,11 @@

Changelog

-

dandelion Version 1.0.0

+

dandelionR Version 1.0.0

Bioconductor version.

-

dandelionR Version 0.99.8 (2025-02-08)

+

dandelionR Version 0.99.9 (2025-02-08)

Updated to address Bioconductor submission review comments. https://github.com/tuonglab/dandelionR/issues/56

diff --git a/pkgdown.yml b/pkgdown.yml index 7d98a36..3c6ca63 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,4 +4,4 @@ pkgdown_sha: ~ articles: dandelionR: dandelionR.html vignette_reproduce_original: vignette_reproduce_original.html -last_built: 2025-02-08T02:39Z +last_built: 2025-02-08T02:47Z diff --git a/reference/chainAssign.html b/reference/chainAssign.html index 5318fcf..a88c2fa 100644 --- a/reference/chainAssign.html +++ b/reference/chainAssign.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9
diff --git a/reference/dandelionR.html b/reference/dandelionR.html index e271799..aa91095 100644 --- a/reference/dandelionR.html +++ b/reference/dandelionR.html @@ -21,7 +21,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/demo_airr.html b/reference/demo_airr.html index ea16dc6..eac3f47 100644 --- a/reference/demo_airr.html +++ b/reference/demo_airr.html @@ -24,7 +24,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/demo_sce.html b/reference/demo_sce.html index cbef51c..8509cf8 100644 --- a/reference/demo_sce.html +++ b/reference/demo_sce.html @@ -23,7 +23,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/differentiationProbabilities.html b/reference/differentiationProbabilities.html index 2ffdb27..09db7d9 100644 --- a/reference/differentiationProbabilities.html +++ b/reference/differentiationProbabilities.html @@ -19,7 +19,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-KNNind.html b/reference/dot-KNNind.html index 1306f7f..9b42915 100644 --- a/reference/dot-KNNind.html +++ b/reference/dot-KNNind.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-addColData.html b/reference/dot-addColData.html index 0e7ec90..137a607 100644 --- a/reference/dot-addColData.html +++ b/reference/dot-addColData.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-allowedChain.html b/reference/dot-allowedChain.html index fb49a43..90e8298 100644 --- a/reference/dot-allowedChain.html +++ b/reference/dot-allowedChain.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-calDif.html b/reference/dot-calDif.html index 1afe2ae..df35bc2 100644 --- a/reference/dot-calDif.html +++ b/reference/dot-calDif.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-classCheck.html b/reference/dot-classCheck.html index 3cad207..c181a0a 100644 --- a/reference/dot-classCheck.html +++ b/reference/dot-classCheck.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-collapse_nested_list.html b/reference/dot-collapse_nested_list.html index 0efa8ae..056f99c 100644 --- a/reference/dot-collapse_nested_list.html +++ b/reference/dot-collapse_nested_list.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-constructMarkovChain.html b/reference/dot-constructMarkovChain.html index 0fa0796..b1456d4 100644 --- a/reference/dot-constructMarkovChain.html +++ b/reference/dot-constructMarkovChain.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-determExtractColN.html b/reference/dot-determExtractColN.html index 85dccf8..c396147 100644 --- a/reference/dot-determExtractColN.html +++ b/reference/dot-determExtractColN.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-determTerminal.html b/reference/dot-determTerminal.html index c6709d9..ad70622 100644 --- a/reference/dot-determTerminal.html +++ b/reference/dot-determTerminal.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-determineMultiscaleSpace.html b/reference/dot-determineMultiscaleSpace.html index 4abe669..b6955de 100644 --- a/reference/dot-determineMultiscaleSpace.html +++ b/reference/dot-determineMultiscaleSpace.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-extractVdj.html b/reference/dot-extractVdj.html index 41397d5..e016854 100644 --- a/reference/dot-extractVdj.html +++ b/reference/dot-extractVdj.html @@ -18,7 +18,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-featureSpaceConstruct.html b/reference/dot-featureSpaceConstruct.html index d7b7c45..3f593ac 100644 --- a/reference/dot-featureSpaceConstruct.html +++ b/reference/dot-featureSpaceConstruct.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-filterCells.html b/reference/dot-filterCells.html index 89c1fe2..3de9e3f 100644 --- a/reference/dot-filterCells.html +++ b/reference/dot-filterCells.html @@ -19,7 +19,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-filterProductivity.html b/reference/dot-filterProductivity.html index 473e03e..53c0e83 100644 --- a/reference/dot-filterProductivity.html +++ b/reference/dot-filterProductivity.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-filterUnmapped.html b/reference/dot-filterUnmapped.html index 674d4a4..b93f33f 100644 --- a/reference/dot-filterUnmapped.html +++ b/reference/dot-filterUnmapped.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-findNewWaypoints.html b/reference/dot-findNewWaypoints.html index fef0a4c..2c2e4b3 100644 --- a/reference/dot-findNewWaypoints.html +++ b/reference/dot-findNewWaypoints.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-generateExtractColumn.html b/reference/dot-generateExtractColumn.html index 74bfd8d..d4bbe9a 100644 --- a/reference/dot-generateExtractColumn.html +++ b/reference/dot-generateExtractColumn.html @@ -18,7 +18,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-generateExtractName.html b/reference/dot-generateExtractName.html index 24bddc2..8eaa7a7 100644 --- a/reference/dot-generateExtractName.html +++ b/reference/dot-generateExtractName.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-getPbs.html b/reference/dot-getPbs.html index a909994..34a8ea6 100644 --- a/reference/dot-getPbs.html +++ b/reference/dot-getPbs.html @@ -18,7 +18,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-getPbsCol.html b/reference/dot-getPbsCol.html index f8a5ce8..902ac7b 100644 --- a/reference/dot-getPbsCol.html +++ b/reference/dot-getPbsCol.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-getPbsPerCol.html b/reference/dot-getPbsPerCol.html index d822391..48ce0be 100644 --- a/reference/dot-getPbsPerCol.html +++ b/reference/dot-getPbsPerCol.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-maxMinSampling.html b/reference/dot-maxMinSampling.html index eeabb30..40dee07 100644 --- a/reference/dot-maxMinSampling.html +++ b/reference/dot-maxMinSampling.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-minMaxScale.html b/reference/dot-minMaxScale.html index db2fff2..a998d95 100644 --- a/reference/dot-minMaxScale.html +++ b/reference/dot-minMaxScale.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-normalizeFeatureSpace.html b/reference/dot-normalizeFeatureSpace.html index a727829..2cc459f 100644 --- a/reference/dot-normalizeFeatureSpace.html +++ b/reference/dot-normalizeFeatureSpace.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-normalizePerVDJ.html b/reference/dot-normalizePerVDJ.html index 5cc5c7b..bd77b6b 100644 --- a/reference/dot-normalizePerVDJ.html +++ b/reference/dot-normalizePerVDJ.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-packFeatureSpace.html b/reference/dot-packFeatureSpace.html index c091a89..5debdb4 100644 --- a/reference/dot-packFeatureSpace.html +++ b/reference/dot-packFeatureSpace.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-removeEdge.html b/reference/dot-removeEdge.html index 6c39c92..3fded01 100644 --- a/reference/dot-removeEdge.html +++ b/reference/dot-removeEdge.html @@ -18,7 +18,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-subsetSce.html b/reference/dot-subsetSce.html index 5fc7bf6..9fbf949 100644 --- a/reference/dot-subsetSce.html +++ b/reference/dot-subsetSce.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-terminalStateFromMarkovChain.html b/reference/dot-terminalStateFromMarkovChain.html index d20429d..9d77f2b 100644 --- a/reference/dot-terminalStateFromMarkovChain.html +++ b/reference/dot-terminalStateFromMarkovChain.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-typeCheck.html b/reference/dot-typeCheck.html index 4c30f55..373ff2a 100644 --- a/reference/dot-typeCheck.html +++ b/reference/dot-typeCheck.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/dot-waypiontsPerCol.html b/reference/dot-waypiontsPerCol.html index e1cf902..71d42ec 100644 --- a/reference/dot-waypiontsPerCol.html +++ b/reference/dot-waypiontsPerCol.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/formatVdj.html b/reference/formatVdj.html index 1b8da79..4cd9d80 100644 --- a/reference/formatVdj.html +++ b/reference/formatVdj.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/index.html b/reference/index.html index 10e6450..d3cee48 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/markovProbability.html b/reference/markovProbability.html index e9f8249..bb9debd 100644 --- a/reference/markovProbability.html +++ b/reference/markovProbability.html @@ -18,7 +18,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/miloUmap.html b/reference/miloUmap.html index 048976a..64bafa5 100644 --- a/reference/miloUmap.html +++ b/reference/miloUmap.html @@ -18,7 +18,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/projectProbability.html b/reference/projectProbability.html index 06b0150..b07670c 100644 --- a/reference/projectProbability.html +++ b/reference/projectProbability.html @@ -18,7 +18,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/projectPseudotimeToCell.html b/reference/projectPseudotimeToCell.html index eceb319..49c99fc 100644 --- a/reference/projectPseudotimeToCell.html +++ b/reference/projectPseudotimeToCell.html @@ -19,7 +19,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/sce_vdj.html b/reference/sce_vdj.html index bee1963..54428ff 100644 --- a/reference/sce_vdj.html +++ b/reference/sce_vdj.html @@ -21,7 +21,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/setupVdjPseudobulk.html b/reference/setupVdjPseudobulk.html index 4e48684..e5e84e3 100644 --- a/reference/setupVdjPseudobulk.html +++ b/reference/setupVdjPseudobulk.html @@ -19,7 +19,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/splitCTgene.html b/reference/splitCTgene.html index 40e32e5..ace52a6 100644 --- a/reference/splitCTgene.html +++ b/reference/splitCTgene.html @@ -17,7 +17,7 @@ dandelionR - 0.99.8 + 0.99.9 diff --git a/reference/vdjPseudobulk.html b/reference/vdjPseudobulk.html index b3ed5ca..07f5c8f 100644 --- a/reference/vdjPseudobulk.html +++ b/reference/vdjPseudobulk.html @@ -19,7 +19,7 @@ dandelionR - 0.99.8 + 0.99.9