Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/articles/Intro_qsvaR.html b/articles/Intro_qsvaR.html index 8a49326..695a0d4 100644 --- a/articles/Intro_qsvaR.html +++ b/articles/Intro_qsvaR.html @@ -6,7 +6,7 @@vignettes/Intro_qsvaR.Rmd
Intro_qsvaR.RmdqsvaR#> Stolz JM, Tnani H, Collado-Torres L (2024). _qsvaR_.
#> doi:10.18129/B9.bioc.qsvaR <https://doi.org/10.18129/B9.bioc.qsvaR>,
#> https://github.com/LieberInstitute/qsvaR/qsvaR - R package version
-#> 1.7.0, <http://www.bioconductor.org/packages/qsvaR>.
+#> 1.9.0, <http://www.bioconductor.org/packages/qsvaR>.
#>
#> Stolz JM, Tnani H, Tao R, Jaffe AE, Collado-Torres L (2024). "qsvaR."
#> _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
@@ -560,10 +560,10 @@ Date the vignette was generated.
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@@ -752,14 +753,14 @@ BibliographyBiocStyle
(Oleś, 2023) with knitr (Xie,
-2023) and rmarkdown
-(Allaire, Xie, Dervieux et al., 2023) running behind the scenes.
+2024) and rmarkdown
+(Allaire, Xie, Dervieux et al., 2024) running behind the scenes.
Citations made with RefManageR
(McLean, 2017).
-[1]
+[1]
J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.25. 2023. URL:
+for R. R package version 2.26. 2024. URL:
https://github.com/rstudio/rmarkdown.
@@ -801,10 +802,10 @@
Bibliographyhttps://bioconductor.org/packages/BiocStyle.
-[7]
+[7]
R Core Team. R: A Language and Environment for Statistical
Computing. R Foundation for Statistical Computing. Vienna, Austria,
-2023. URL:
+2024. URL:
https://www.R-project.org/.
@@ -815,17 +816,14 @@
Bibliography10.1093/nar/gkv007.
-[9]
+[9]
L. Shepherd and M. Morgan. BiocFileCache: Manage Files Across
-Sessions. R package version 2.10.1. 2023. DOI:
-10.18129/B9.bioc.BiocFileCache.
-URL:
-https://bioconductor.org/packages/BiocFileCache.
+Sessions. R package version 2.10.2. 2024.
[10]
J. M. Stolz, H. Tnani, and L. Collado-Torres. qsvaR. https://github.com/LieberInstitute/qsvaR/qsvaR - R
-package version 1.7.0. 2024. DOI:
+package version 1.9.0. 2024. DOI:
10.18129/B9.bioc.qsvaR.
URL:
http://www.bioconductor.org/packages/qsvaR.
@@ -849,9 +847,9 @@
Bibliographyhttps://github.com/r-lib/sessioninfo#readme.
-[14]
+[14]
Y. Xie. knitr: A General-Purpose Package for Dynamic Report
-Generation in R. R package version 1.45. 2023. URL:
+Generation in R. R package version 1.46. 2024. URL:
https://yihui.org/knitr/.
@@ -874,7 +872,7 @@ Bibliography
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/articles/Intro_qsvaR_files/figure-html/Generate DEqual with qSVs-1.png b/articles/Intro_qsvaR_files/figure-html/Generate DEqual with qSVs-1.png
index f975550..50e815b 100644
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diff --git a/articles/Intro_qsvaR_files/figure-html/Generate DEqual without qSVs-1.png b/articles/Intro_qsvaR_files/figure-html/Generate DEqual without qSVs-1.png
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diff --git a/articles/index.html b/articles/index.html
index 2f3051d..cb5e032 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,5 +1,5 @@
-Articles • qsvaR Articles • qsvaR
@@ -17,7 +17,7 @@
@@ -72,7 +72,7 @@ All vignettes
diff --git a/authors.html b/authors.html
index d4d11a3..58542f6 100644
--- a/authors.html
+++ b/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • qsvaR Authors and Citation • qsvaR
@@ -17,7 +17,7 @@
@@ -54,7 +54,7 @@
diff --git a/index.html b/index.html
index 69717bf..caf2c48 100644
--- a/index.html
+++ b/index.html
@@ -6,18 +6,14 @@
Generate Quality Surrogate Variable Analysis for Degradation Correction • qsvaR
-
+
-
+
Changelog • qsvaR Changelog • qsvaR
@@ -17,7 +17,7 @@
@@ -108,7 +108,7 @@ qsvaR 0.99.0
diff --git a/pkgdown.yml b/pkgdown.yml
index a202eb4..9c72fd1 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,7 +1,7 @@
pandoc: 3.1.1
-pkgdown: 2.0.7
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
Intro_qsvaR: Intro_qsvaR.html
-last_built: 2024-01-17T16:59Z
+last_built: 2024-05-03T14:21Z
diff --git a/reference/DEqual-1.png b/reference/DEqual-1.png
index 42cca1b..9fb44b3 100644
Binary files a/reference/DEqual-1.png and b/reference/DEqual-1.png differ
diff --git a/reference/DEqual.html b/reference/DEqual.html
index 66769a2..c4d8b88 100644
--- a/reference/DEqual.html
+++ b/reference/DEqual.html
@@ -1,5 +1,5 @@
-Differential expression quality (DEqual) plot — DEqual • qsvaR Differential expression quality (DEqual) plot — DEqual • qsvaR
qsvaR
- 1.7.0
+ 1.9.0
@@ -129,7 +129,7 @@ Examples
diff --git a/reference/check_tx_names.html b/reference/check_tx_names.html
index 838eac7..f837909 100644
--- a/reference/check_tx_names.html
+++ b/reference/check_tx_names.html
@@ -1,5 +1,5 @@
-Check validity of transcript vectors — check_tx_names • qsvaR Check validity of transcript vectors — check_tx_names • qsvaR
@@ -17,7 +17,7 @@
@@ -1598,7 +1598,7 @@ Examples
diff --git a/reference/covComb_tx_deg.html b/reference/covComb_tx_deg.html
index 155b2c3..723688b 100644
--- a/reference/covComb_tx_deg.html
+++ b/reference/covComb_tx_deg.html
@@ -1,5 +1,5 @@
-RSE object of RNA-seq data that serves as output for degradation analysis — covComb_tx_deg • qsvaR RSE object of RNA-seq data that serves as output for degradation analysis — covComb_tx_deg • qsvaR Degradation time t-statistics — degradation_tstats • qsvaR Degradation time t-statistics — degradation_tstats • qsvaR
qsvaR
- 1.7.0
+ 1.9.0
@@ -93,7 +93,7 @@ See also
diff --git a/reference/getDegTx.html b/reference/getDegTx.html
index 46bb3ab..e9366db 100644
--- a/reference/getDegTx.html
+++ b/reference/getDegTx.html
@@ -1,5 +1,5 @@
-Obtain expression matrix for degraded transcripts — getDegTx • qsvaR Obtain expression matrix for degraded transcripts — getDegTx • qsvaR PCs from transcripts — getPCs • qsvaR PCs from transcripts — getPCs • qsvaR
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ Examples
diff --git a/reference/get_qsvs.html b/reference/get_qsvs.html
index 1a772a8..e4b5135 100644
--- a/reference/get_qsvs.html
+++ b/reference/get_qsvs.html
@@ -1,5 +1,5 @@
-Generate matrix of qsvs — get_qsvs • qsvaR Generate matrix of qsvs — get_qsvs • qsvaR Function reference • qsvaR Function reference • qsvaR
@@ -17,7 +17,7 @@
@@ -117,7 +117,7 @@ All functions
diff --git a/reference/k_qsvs.html b/reference/k_qsvs.html
index 54d721a..bb61559 100644
--- a/reference/k_qsvs.html
+++ b/reference/k_qsvs.html
@@ -1,5 +1,5 @@
-Apply num.sv algorithm to determine the number of pcs to be included — k_qsvs • qsvaR Apply num.sv algorithm to determine the number of pcs to be included — k_qsvs • qsvaR
@@ -17,7 +17,7 @@
@@ -119,7 +119,7 @@ Examples
diff --git a/reference/qSVA.html b/reference/qSVA.html
index b97936c..7c92275 100644
--- a/reference/qSVA.html
+++ b/reference/qSVA.html
@@ -1,5 +1,5 @@
-A wrapper function used to perform qSVA in one step. — qSVA • qsvaR A wrapper function used to perform qSVA in one step. — qSVA • qsvaR
@@ -17,7 +17,7 @@
@@ -324,7 +324,7 @@ Examples
diff --git a/reference/select_transcripts.html b/reference/select_transcripts.html
index 461dfa8..0a4b88d 100644
--- a/reference/select_transcripts.html
+++ b/reference/select_transcripts.html
@@ -1,5 +1,5 @@
-Select transcripts associated with degradation — select_transcripts • qsvaR Select transcripts associated with degradation — select_transcripts • qsvaR
@@ -17,7 +17,7 @@
@@ -1418,7 +1418,7 @@ Examples
diff --git a/reference/transcripts.html b/reference/transcripts.html
index 3127c5f..9edfa39 100644
--- a/reference/transcripts.html
+++ b/reference/transcripts.html
@@ -1,5 +1,5 @@
-Transcripts for Degradation Models — transcripts • qsvaR
@@ -98,7 +98,7 @@ See also