From c3a85515ad54cb5abc4251862155f0ec6d082f54 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Wed, 24 Apr 2024 17:39:46 +0000 Subject: [PATCH] cli-14512-885 --- 404.html | 2 +- articles/differential_signal_fixed.html | 10 +++++----- articles/differential_signal_sliding.html | 10 +++++----- articles/index.html | 2 +- articles/range_based_functions.html | 8 ++++---- authors.html | 6 +++--- index.html | 2 +- news/index.html | 2 +- pkgdown.yml | 4 ++-- reference/addDiffStatus-methods.html | 2 +- reference/as_tibble.html | 2 +- reference/bestOverlap-methods.html | 2 +- reference/chopMC.html | 2 +- reference/colToRanges-methods.html | 2 +- reference/collapseGenes.html | 2 +- reference/cytobands.html | 2 +- reference/defineRegions.html | 2 +- reference/defineSeqinfo.html | 2 +- reference/distinctMC.html | 2 +- reference/dot-makeFinalProfileHeatmap.html | 2 +- reference/dot-mapFeatures.html | 2 +- reference/dot-mapGi.html | 2 +- reference/dot-mapWithin.html | 2 +- reference/dualFilter.html | 2 +- reference/ex_datasets.html | 2 +- reference/extraChIPs-package.html | 2 +- reference/fitAssayDiff-methods.html | 2 +- reference/fixed_width_datasets.html | 2 +- reference/getProfileData-methods.html | 2 +- reference/grlToSE-methods.html | 2 +- reference/importPeaks.html | 2 +- reference/index.html | 2 +- reference/makeConsensus.html | 2 +- reference/mapByFeature.html | 2 +- reference/mapGrlCols.html | 2 +- reference/mergeByCol-methods.html | 2 +- reference/mergeByHMP-methods.html | 2 +- reference/mergeBySig-methods.html | 2 +- reference/partitionRanges-methods.html | 2 +- reference/plotAssayDensities-methods.html | 2 +- reference/plotAssayHeatmap-methods.html | 2 +- reference/plotAssayPCA-methods.html | 2 +- reference/plotAssayRle-methods.html | 2 +- reference/plotGrlCol.html | 2 +- reference/plotHFGC.html | 2 +- reference/plotOverlaps-methods.html | 2 +- reference/plotPairwise.html | 2 +- reference/plotPie-methods.html | 2 +- reference/plotProfileHeatmap-methods.html | 2 +- reference/plotSplitDonut-methods.html | 2 +- reference/propOverlap-methods.html | 2 +- reference/reduceMC.html | 2 +- reference/setoptsMC-methods.html | 2 +- reference/stitchRanges.html | 2 +- reference/voomWeightsFromCPM.html | 2 +- 55 files changed, 69 insertions(+), 69 deletions(-) diff --git a/404.html b/404.html index 4d4f8a6..09e0d5c 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/articles/differential_signal_fixed.html b/articles/differential_signal_fixed.html index 0ae3efd..d989748 100644 --- a/articles/differential_signal_fixed.html +++ b/articles/differential_signal_fixed.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.8 + 1.7.9 @@ -762,7 +762,7 @@

Session Info## [1] quantro_1.37.0 here_1.0.1 ## [3] ggrepel_0.9.5 glue_1.7.0 ## [5] scales_1.3.0 plyranges_1.23.2 -## [7] extraChIPs_1.7.8 ggside_0.3.1 +## [7] extraChIPs_1.7.9 ggside_0.3.1 ## [9] patchwork_1.2.0 edgeR_4.1.23 ## [11] limma_3.59.8 rtracklayer_1.63.2 ## [13] BiocParallel_1.37.1 csaw_1.37.1 @@ -776,7 +776,7 @@

Session Info## [29] stringr_1.5.1 dplyr_1.1.4 ## [31] purrr_1.0.2 readr_2.1.5 ## [33] tidyr_1.3.1 tibble_3.2.1 -## [35] ggplot2_3.5.0 tidyverse_2.0.0 +## [35] ggplot2_3.5.1 tidyverse_2.0.0 ## [37] BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): @@ -814,9 +814,9 @@

Session Info## [63] beanplot_1.3.1 metapod_1.11.1 ## [65] rjson_0.2.21 codetools_0.2-20 ## [67] data.table_1.15.4 vctrs_0.6.5 -## [69] png_0.1-8 gtable_0.3.4 +## [69] png_0.1-8 gtable_0.3.5 ## [71] cachem_1.0.8 xfun_0.43 -## [73] S4Arrays_1.3.7 survival_3.5-8 +## [73] S4Arrays_1.3.7 survival_3.6-4 ## [75] iterators_1.0.14 statmod_1.5.0 ## [77] GenomicInteractions_1.37.0 nlme_3.1-164 ## [79] bit64_4.0.5 progress_1.2.3 diff --git a/articles/differential_signal_sliding.html b/articles/differential_signal_sliding.html index 946848a..d7ac142 100644 --- a/articles/differential_signal_sliding.html +++ b/articles/differential_signal_sliding.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.8 + 1.7.9 @@ -1300,7 +1300,7 @@

Session Info## [7] mclust_6.1 quantro_1.37.0 ## [9] magrittr_2.0.3 here_1.0.1 ## [11] glue_1.7.0 scales_1.3.0 -## [13] plyranges_1.23.2 extraChIPs_1.7.8 +## [13] plyranges_1.23.2 extraChIPs_1.7.9 ## [15] ggside_0.3.1 patchwork_1.2.0 ## [17] edgeR_4.1.23 limma_3.59.8 ## [19] rtracklayer_1.63.2 BiocParallel_1.37.1 @@ -1314,7 +1314,7 @@

Session Info## [35] forcats_1.0.0 stringr_1.5.1 ## [37] dplyr_1.1.4 purrr_1.0.2 ## [39] readr_2.1.5 tidyr_1.3.1 -## [41] tibble_3.2.1 ggplot2_3.5.0 +## [41] tibble_3.2.1 ggplot2_3.5.1 ## [43] tidyverse_2.0.0 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): @@ -1351,9 +1351,9 @@

Session Info## [61] metapod_1.11.1 rjson_0.2.21 ## [63] codetools_0.2-20 data.table_1.15.4 ## [65] vctrs_0.6.5 png_0.1-8 -## [67] gtable_0.3.4 cachem_1.0.8 +## [67] gtable_0.3.5 cachem_1.0.8 ## [69] xfun_0.43 S4Arrays_1.3.7 -## [71] survival_3.5-8 iterators_1.0.14 +## [71] survival_3.6-4 iterators_1.0.14 ## [73] statmod_1.5.0 GenomicInteractions_1.37.0 ## [75] nlme_3.1-164 bit64_4.0.5 ## [77] progress_1.2.3 filelock_1.0.3 diff --git a/articles/index.html b/articles/index.html index 8a96baa..635f008 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/articles/range_based_functions.html b/articles/range_based_functions.html index 9dada7f..c52749d 100644 --- a/articles/range_based_functions.html +++ b/articles/range_based_functions.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.8 + 1.7.9 @@ -666,7 +666,7 @@

Session Info## [8] base ## ## other attached packages: -## [1] plyranges_1.23.2 extraChIPs_1.7.8 +## [1] plyranges_1.23.2 extraChIPs_1.7.9 ## [3] SummarizedExperiment_1.33.3 Biobase_2.63.1 ## [5] MatrixGenerics_1.15.1 matrixStats_1.3.0 ## [7] ggside_0.3.1 GenomicRanges_1.55.4 @@ -676,7 +676,7 @@

Session Info## [15] forcats_1.0.0 stringr_1.5.1 ## [17] dplyr_1.1.4 purrr_1.0.2 ## [19] readr_2.1.5 tidyr_1.3.1 -## [21] tibble_3.2.1 ggplot2_3.5.0 +## [21] tibble_3.2.1 ggplot2_3.5.1 ## [23] tidyverse_2.0.0 BiocStyle_2.31.0 ## ## loaded via a namespace (and not attached): @@ -722,7 +722,7 @@

Session Info## [79] prettyunits_1.2.0 InteractionSet_1.31.0 ## [81] httr_1.4.7 htmlwidgets_1.6.4 ## [83] S4Arrays_1.3.7 pkgconfig_2.0.3 -## [85] gtable_0.3.4 blob_1.2.4 +## [85] gtable_0.3.5 blob_1.2.4 ## [87] XVector_0.43.1 htmltools_0.5.8.1 ## [89] bookdown_0.39 ProtGenerics_1.35.4 ## [91] scales_1.3.0 png_0.1-8 diff --git a/authors.html b/authors.html index a686e24..ff19d62 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 @@ -79,13 +79,13 @@

Citation

Pederson S (2024). extraChIPs: Additional functions for working with ChIP-Seq data. -R package version 1.7.8, https://github.com/smped/extraChIPs. +R package version 1.7.9, https://github.com/smped/extraChIPs. 

@Manual{,
   title = {extraChIPs: Additional functions for working with ChIP-Seq data},
   author = {Stevie Pederson},
   year = {2024},
-  note = {R package version 1.7.8},
+  note = {R package version 1.7.9},
   url = {https://github.com/smped/extraChIPs},
 }
diff --git a/index.html b/index.html index aae4ad8..b4a3e28 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/news/index.html b/news/index.html index cfe63f1..9c7acef 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/pkgdown.yml b/pkgdown.yml index a9cefba..79f4f27 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,9 +1,9 @@ pandoc: 3.1.1 pkgdown: 2.0.9.9000 -pkgdown_sha: 910bb1d4dc7068926c05d625b9794a51bebc3237 +pkgdown_sha: 8b605f2590751adb9bb3d6b203657628c04ba51d articles: differential_signal_fixed: differential_signal_fixed.html differential_signal_sliding: differential_signal_sliding.html range_based_functions: range_based_functions.html -last_built: 2024-04-22T14:54Z +last_built: 2024-04-24T17:37Z diff --git a/reference/addDiffStatus-methods.html b/reference/addDiffStatus-methods.html index a5d62e7..0ddb046 100644 --- a/reference/addDiffStatus-methods.html +++ b/reference/addDiffStatus-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/as_tibble.html b/reference/as_tibble.html index 4210a94..a003c93 100644 --- a/reference/as_tibble.html +++ b/reference/as_tibble.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/bestOverlap-methods.html b/reference/bestOverlap-methods.html index 0128c9c..f2e79d6 100644 --- a/reference/bestOverlap-methods.html +++ b/reference/bestOverlap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/chopMC.html b/reference/chopMC.html index 9f55239..85cd9ef 100644 --- a/reference/chopMC.html +++ b/reference/chopMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/colToRanges-methods.html b/reference/colToRanges-methods.html index 0234b9f..c150e91 100644 --- a/reference/colToRanges-methods.html +++ b/reference/colToRanges-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/collapseGenes.html b/reference/collapseGenes.html index 6860fb6..b90f8b7 100644 --- a/reference/collapseGenes.html +++ b/reference/collapseGenes.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/cytobands.html b/reference/cytobands.html index 8621db9..8824db3 100644 --- a/reference/cytobands.html +++ b/reference/cytobands.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/defineRegions.html b/reference/defineRegions.html index 5cbee09..1ab7c74 100644 --- a/reference/defineRegions.html +++ b/reference/defineRegions.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/defineSeqinfo.html b/reference/defineSeqinfo.html index b7bc92c..be02e56 100644 --- a/reference/defineSeqinfo.html +++ b/reference/defineSeqinfo.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/distinctMC.html b/reference/distinctMC.html index e0f37d1..aa7b390 100644 --- a/reference/distinctMC.html +++ b/reference/distinctMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/dot-makeFinalProfileHeatmap.html b/reference/dot-makeFinalProfileHeatmap.html index ea39157..4a324c5 100644 --- a/reference/dot-makeFinalProfileHeatmap.html +++ b/reference/dot-makeFinalProfileHeatmap.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/dot-mapFeatures.html b/reference/dot-mapFeatures.html index 5f21224..00ceedb 100644 --- a/reference/dot-mapFeatures.html +++ b/reference/dot-mapFeatures.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/dot-mapGi.html b/reference/dot-mapGi.html index 0d03459..be23e28 100644 --- a/reference/dot-mapGi.html +++ b/reference/dot-mapGi.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/dot-mapWithin.html b/reference/dot-mapWithin.html index 913d83c..b367d32 100644 --- a/reference/dot-mapWithin.html +++ b/reference/dot-mapWithin.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/dualFilter.html b/reference/dualFilter.html index 17a8a12..3cf9dcd 100644 --- a/reference/dualFilter.html +++ b/reference/dualFilter.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/ex_datasets.html b/reference/ex_datasets.html index 48f4d29..fb9cfab 100644 --- a/reference/ex_datasets.html +++ b/reference/ex_datasets.html @@ -37,7 +37,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/extraChIPs-package.html b/reference/extraChIPs-package.html index 23eeaec..35b7b07 100644 --- a/reference/extraChIPs-package.html +++ b/reference/extraChIPs-package.html @@ -19,7 +19,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/fitAssayDiff-methods.html b/reference/fitAssayDiff-methods.html index b107eb0..7d45220 100644 --- a/reference/fitAssayDiff-methods.html +++ b/reference/fitAssayDiff-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/fixed_width_datasets.html b/reference/fixed_width_datasets.html index 79f319d..71295d7 100644 --- a/reference/fixed_width_datasets.html +++ b/reference/fixed_width_datasets.html @@ -19,7 +19,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/getProfileData-methods.html b/reference/getProfileData-methods.html index 990d9cc..ee4bc3b 100644 --- a/reference/getProfileData-methods.html +++ b/reference/getProfileData-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/grlToSE-methods.html b/reference/grlToSE-methods.html index 710160f..266a08b 100644 --- a/reference/grlToSE-methods.html +++ b/reference/grlToSE-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/importPeaks.html b/reference/importPeaks.html index 2d4750b..7573ae4 100644 --- a/reference/importPeaks.html +++ b/reference/importPeaks.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/index.html b/reference/index.html index f167232..f98ee6a 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/makeConsensus.html b/reference/makeConsensus.html index 0493ce4..d8679cb 100644 --- a/reference/makeConsensus.html +++ b/reference/makeConsensus.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/mapByFeature.html b/reference/mapByFeature.html index 61cb985..52073b0 100644 --- a/reference/mapByFeature.html +++ b/reference/mapByFeature.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/mapGrlCols.html b/reference/mapGrlCols.html index f35330a..1321b13 100644 --- a/reference/mapGrlCols.html +++ b/reference/mapGrlCols.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/mergeByCol-methods.html b/reference/mergeByCol-methods.html index 3324a88..0a3f63d 100644 --- a/reference/mergeByCol-methods.html +++ b/reference/mergeByCol-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/mergeByHMP-methods.html b/reference/mergeByHMP-methods.html index cba22e9..61101db 100644 --- a/reference/mergeByHMP-methods.html +++ b/reference/mergeByHMP-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/mergeBySig-methods.html b/reference/mergeBySig-methods.html index f253580..a41d1cf 100644 --- a/reference/mergeBySig-methods.html +++ b/reference/mergeBySig-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/partitionRanges-methods.html b/reference/partitionRanges-methods.html index cc265c6..49fbef8 100644 --- a/reference/partitionRanges-methods.html +++ b/reference/partitionRanges-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotAssayDensities-methods.html b/reference/plotAssayDensities-methods.html index 4126805..338a77a 100644 --- a/reference/plotAssayDensities-methods.html +++ b/reference/plotAssayDensities-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotAssayHeatmap-methods.html b/reference/plotAssayHeatmap-methods.html index df9b3b4..4bfbd27 100644 --- a/reference/plotAssayHeatmap-methods.html +++ b/reference/plotAssayHeatmap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotAssayPCA-methods.html b/reference/plotAssayPCA-methods.html index 78a7e0b..29607df 100644 --- a/reference/plotAssayPCA-methods.html +++ b/reference/plotAssayPCA-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotAssayRle-methods.html b/reference/plotAssayRle-methods.html index 16fd6d9..1c012ae 100644 --- a/reference/plotAssayRle-methods.html +++ b/reference/plotAssayRle-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotGrlCol.html b/reference/plotGrlCol.html index 3a4f8f2..65d2d85 100644 --- a/reference/plotGrlCol.html +++ b/reference/plotGrlCol.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotHFGC.html b/reference/plotHFGC.html index c6d4274..66ed3c8 100644 --- a/reference/plotHFGC.html +++ b/reference/plotHFGC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotOverlaps-methods.html b/reference/plotOverlaps-methods.html index 3e6f966..8c94cff 100644 --- a/reference/plotOverlaps-methods.html +++ b/reference/plotOverlaps-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotPairwise.html b/reference/plotPairwise.html index 7b2f307..75194db 100644 --- a/reference/plotPairwise.html +++ b/reference/plotPairwise.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotPie-methods.html b/reference/plotPie-methods.html index eae4c39..ff3f88c 100644 --- a/reference/plotPie-methods.html +++ b/reference/plotPie-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotProfileHeatmap-methods.html b/reference/plotProfileHeatmap-methods.html index fbb15fb..a891aef 100644 --- a/reference/plotProfileHeatmap-methods.html +++ b/reference/plotProfileHeatmap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/plotSplitDonut-methods.html b/reference/plotSplitDonut-methods.html index 03ef066..348a0f7 100644 --- a/reference/plotSplitDonut-methods.html +++ b/reference/plotSplitDonut-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/propOverlap-methods.html b/reference/propOverlap-methods.html index a39baf7..41169e1 100644 --- a/reference/propOverlap-methods.html +++ b/reference/propOverlap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/reduceMC.html b/reference/reduceMC.html index 9b97588..030a940 100644 --- a/reference/reduceMC.html +++ b/reference/reduceMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/setoptsMC-methods.html b/reference/setoptsMC-methods.html index 6b9b3e3..4d8883f 100644 --- a/reference/setoptsMC-methods.html +++ b/reference/setoptsMC-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/stitchRanges.html b/reference/stitchRanges.html index f0d98d5..68b1c00 100644 --- a/reference/stitchRanges.html +++ b/reference/stitchRanges.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.8 + 1.7.9 diff --git a/reference/voomWeightsFromCPM.html b/reference/voomWeightsFromCPM.html index cb5071e..83d346d 100644 --- a/reference/voomWeightsFromCPM.html +++ b/reference/voomWeightsFromCPM.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.8 + 1.7.9