From 05c61cce85cf8ee40585e1eb24a6020855763738 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 19 Feb 2024 04:18:58 +0000 Subject: [PATCH] cli-154-233 --- 404.html | 2 +- TODO.html | 2 +- articles/creating_a_new_reference.html | 12 ++++++------ articles/index.html | 2 +- authors.html | 6 +++--- index.html | 2 +- news/index.html | 2 +- pkgdown.yml | 4 ++-- reference/genomogrify-methods.html | 2 +- reference/indelcator-methods.html | 2 +- reference/index.html | 2 +- reference/overlapsByVar-methods.html | 2 +- reference/owl-methods.html | 2 +- reference/parY-methods.html | 2 +- reference/sjFromExons.html | 2 +- reference/transmogR-package.html | 2 +- reference/transmogrify-methods.html | 2 +- reference/upsetVarByCol.html | 2 +- reference/varTypes.html | 2 +- 19 files changed, 27 insertions(+), 27 deletions(-) diff --git a/404.html b/404.html index dc76c77..13174f4 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/TODO.html b/TODO.html index 90a3151..4782272 100644 --- a/TODO.html +++ b/TODO.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/articles/creating_a_new_reference.html b/articles/creating_a_new_reference.html index 712e7ca..ac7315b 100644 --- a/articles/creating_a_new_reference.html +++ b/articles/creating_a_new_reference.html @@ -33,7 +33,7 @@ transmogR - 0.99.2 + 0.99.3 @@ -531,15 +531,15 @@

Session info## [8] base ## ## other attached packages: -## [1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.1 -## [3] BiocIO_1.12.0 transmogR_0.99.2 +## [1] BSgenome.Hsapiens.UCSC.hg38_1.4.5 BSgenome_1.70.2 +## [3] BiocIO_1.12.0 transmogR_0.99.3 ## [5] extraChIPs_1.6.0 tibble_3.2.1 ## [7] ggside_0.2.3 ggplot2_3.4.4 ## [9] BiocParallel_1.36.0 rtracklayer_1.62.0 ## [11] VariantAnnotation_1.48.1 Rsamtools_2.18.0 ## [13] Biostrings_2.70.2 XVector_0.42.0 ## [15] SummarizedExperiment_1.32.0 Biobase_2.62.0 -## [17] GenomicRanges_1.54.1 GenomeInfoDb_1.38.5 +## [17] GenomicRanges_1.54.1 GenomeInfoDb_1.38.6 ## [19] IRanges_2.36.0 S4Vectors_0.40.2 ## [21] MatrixGenerics_1.14.0 matrixStats_1.2.0 ## [23] BiocGenerics_0.48.1 BiocStyle_2.30.0 @@ -548,7 +548,7 @@

Session info## [1] bitops_1.0-7 filelock_1.0.3 ## [3] polyclip_1.10-6 XML_3.99-0.16.1 ## [5] rpart_4.1.23 lifecycle_1.0.4 -## [7] edgeR_4.0.14 doParallel_1.0.17 +## [7] edgeR_4.0.15 doParallel_1.0.17 ## [9] MASS_7.3-60.0.1 lattice_0.22-5 ## [11] ensembldb_2.26.0 backports_1.4.1 ## [13] magrittr_2.0.3 limma_3.58.1 @@ -575,7 +575,7 @@

Session info## [55] tools_4.3.2 progress_1.2.3 ## [57] ragg_1.2.7 Rcpp_1.0.12 ## [59] glue_1.7.0 gridExtra_2.3 -## [61] SparseArray_1.2.3 xfun_0.41 +## [61] SparseArray_1.2.4 xfun_0.42 ## [63] dplyr_1.1.4 withr_3.0.0 ## [65] formatR_1.14 BiocManager_1.30.22 ## [67] fastmap_1.1.1 latticeExtra_0.6-30 diff --git a/articles/index.html b/articles/index.html index cb78716..64b4909 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/authors.html b/authors.html index 409b3c1..e0fc53f 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 @@ -73,13 +73,13 @@

Citation

Pederson S (2024). transmogR: Modify a set of reference sequences using a set of variants. -R package version 0.99.2, https://github.com/smped/transmogR. +R package version 0.99.3, https://github.com/smped/transmogR. 

@Manual{,
   title = {transmogR: Modify a set of reference sequences using a set of variants},
   author = {Stevie Pederson},
   year = {2024},
-  note = {R package version 0.99.2},
+  note = {R package version 0.99.3},
   url = {https://github.com/smped/transmogR},
 }
diff --git a/index.html b/index.html index b2c1b22..366a346 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/news/index.html b/news/index.html index b9d142a..c1c2cba 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/pkgdown.yml b/pkgdown.yml index 075b8a9..679f7ef 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,7 @@ pandoc: 3.1.1 pkgdown: 2.0.7.9000 -pkgdown_sha: 548a9493b72ff93d3ed8392d4ad30b77d8b15fa5 +pkgdown_sha: 3979e7c0afbba4503248dc8a6d04fe0a2e03f26f articles: creating_a_new_reference: creating_a_new_reference.html -last_built: 2024-02-02T08:08Z +last_built: 2024-02-19T04:18Z diff --git a/reference/genomogrify-methods.html b/reference/genomogrify-methods.html index d781dfb..7d1279b 100644 --- a/reference/genomogrify-methods.html +++ b/reference/genomogrify-methods.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/indelcator-methods.html b/reference/indelcator-methods.html index 61b97a9..c45d056 100644 --- a/reference/indelcator-methods.html +++ b/reference/indelcator-methods.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/index.html b/reference/index.html index 91a00dc..939d39d 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/overlapsByVar-methods.html b/reference/overlapsByVar-methods.html index 535fc69..4526511 100644 --- a/reference/overlapsByVar-methods.html +++ b/reference/overlapsByVar-methods.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/owl-methods.html b/reference/owl-methods.html index 578af2c..7c5c83c 100644 --- a/reference/owl-methods.html +++ b/reference/owl-methods.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/parY-methods.html b/reference/parY-methods.html index c4ba859..3aabc76 100644 --- a/reference/parY-methods.html +++ b/reference/parY-methods.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/sjFromExons.html b/reference/sjFromExons.html index d4bd9ef..f170af4 100644 --- a/reference/sjFromExons.html +++ b/reference/sjFromExons.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/transmogR-package.html b/reference/transmogR-package.html index 52cc61d..973c2e3 100644 --- a/reference/transmogR-package.html +++ b/reference/transmogR-package.html @@ -18,7 +18,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/transmogrify-methods.html b/reference/transmogrify-methods.html index 5171de6..bbf47aa 100644 --- a/reference/transmogrify-methods.html +++ b/reference/transmogrify-methods.html @@ -18,7 +18,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/upsetVarByCol.html b/reference/upsetVarByCol.html index e1a93d8..56d72ce 100644 --- a/reference/upsetVarByCol.html +++ b/reference/upsetVarByCol.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3 diff --git a/reference/varTypes.html b/reference/varTypes.html index bbcf2d6..15305e6 100644 --- a/reference/varTypes.html +++ b/reference/varTypes.html @@ -17,7 +17,7 @@ transmogR - 0.99.2 + 0.99.3