From a927ab960819f802994517305e9b561e7f7dc5e1 Mon Sep 17 00:00:00 2001 From: HDash <16350928+HDash@users.noreply.github.com> Date: Thu, 25 Jul 2024 17:21:16 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20neurogen?= =?UTF-8?q?omics/MotifPeeker@0e90310e53a1dd32c340e493b24530f8066b900c=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/MotifPeeker.html | 4 ++-- articles/docker.html | 2 +- articles/examples.html | 2 +- articles/troubleshooting.html | 2 +- index.html | 2 +- pkgdown.yml | 2 +- reference/MotifPeeker.html | 2 +- reference/check_ENCODE.html | 2 +- reference/check_JASPAR.html | 2 +- reference/find_motifs.html | 8 ++++---- reference/get_JASPARCORE.html | 4 ++-- reference/plot_enrichment_individual.html | 2 +- reference/save_peak_file.html | 2 +- reference/to_plotly.html | 2 +- search.json | 2 +- 15 files changed, 20 insertions(+), 20 deletions(-) diff --git a/articles/MotifPeeker.html b/articles/MotifPeeker.html index 3de2cb5..eeeb8ba 100644 --- a/articles/MotifPeeker.html +++ b/articles/MotifPeeker.html @@ -74,7 +74,7 @@

Get started

-

Updated: Jul-23-2024

+

Updated: Jul-25-2024

Overview

@@ -289,7 +289,7 @@

Run MotifPeeker= TRUE, verbose = TRUE )

-
## [1] "/tmp/RtmphV8hIE/MotifPeeker_20240723_233807"
+
## [1] "/tmp/RtmpfKPFnV/MotifPeeker_20240725_172020"

Required Inputs

diff --git a/articles/docker.html b/articles/docker.html index 557c858..633c61d 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -74,7 +74,7 @@

Docker/Singularity Containers

-

Updated: Jul-23-2024

+

Updated: Jul-25-2024

Installation

diff --git a/articles/examples.html b/articles/examples.html index 5a30b95..0c3ca4d 100644 --- a/articles/examples.html +++ b/articles/examples.html @@ -74,7 +74,7 @@

Example Reports

-

Updated: Jul-23-2024

+

Updated: Jul-25-2024

MotifPeeker-reports is a public archive for interactive HTML reports generated by MotifPeeker, along with the code used to produce them.

diff --git a/articles/troubleshooting.html b/articles/troubleshooting.html index 69478bd..8089c7b 100644 --- a/articles/troubleshooting.html +++ b/articles/troubleshooting.html @@ -74,7 +74,7 @@

Troubleshooting

-

Updated: Jul-23-2024

+

Updated: Jul-25-2024

This vignette provides troubleshooting tips for common issues encountered when using the MotifPeeker package.

If you encounter an issue that is not covered, please open an issue diff --git a/index.html b/index.html index be24f52..bce9e67 100644 --- a/index.html +++ b/index.html @@ -67,7 +67,7 @@

License: GPL (>= 3)
R build status

-

Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan Skene
Updated: Jul-23-2024

+

Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan Skene
Updated: Jul-25-2024

Introduction

diff --git a/pkgdown.yml b/pkgdown.yml index 71b5b2e..78b5f6a 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: articles/examples: examples.html MotifPeeker: MotifPeeker.html troubleshooting: troubleshooting.html -last_built: 2024-07-23T23:35Z +last_built: 2024-07-25T17:18Z urls: reference: https://neurogenomics.github.io/MotifPeeker/reference article: https://neurogenomics.github.io/MotifPeeker/articles diff --git a/reference/MotifPeeker.html b/reference/MotifPeeker.html index 7457849..dc29cc7 100644 --- a/reference/MotifPeeker.html +++ b/reference/MotifPeeker.html @@ -323,7 +323,7 @@

Examples quiet = TRUE, verbose = FALSE ) -#> [1] "/tmp/RtmpGJSeqg/MotifPeeker_20240723_233610" +#> [1] "/tmp/RtmpzWRxoP/MotifPeeker_20240725_171824"

diff --git a/reference/check_ENCODE.html b/reference/check_ENCODE.html index 0ebdaa2..0f35d59 100644 --- a/reference/check_ENCODE.html +++ b/reference/check_ENCODE.html @@ -84,7 +84,7 @@

Examples check_ENCODE("ENCFF109VAD", expect_format = "bam") } #> BFC2 -#> "/github/home/.cache/R/BiocFileCache/16b53c8047c7_ENCFF109VAD.bam" +#> "/github/home/.cache/R/BiocFileCache/1223251213f4_ENCFF109VAD.bam" diff --git a/reference/check_JASPAR.html b/reference/check_JASPAR.html index b7e026e..3353ff7 100644 --- a/reference/check_JASPAR.html +++ b/reference/check_JASPAR.html @@ -75,7 +75,7 @@

Value

Examples

check_JASPAR("MA1930.2")
 #>                                                               BFC3 
-#> "/github/home/.cache/R/BiocFileCache/16b5798dc716_MA1930.2.jaspar" 
+#> "/github/home/.cache/R/BiocFileCache/122331867ec6_MA1930.2.jaspar"
diff --git a/reference/find_motifs.html b/reference/find_motifs.html index 3e1c573..69ce124 100644 --- a/reference/find_motifs.html +++ b/reference/find_motifs.html @@ -144,8 +144,8 @@

Examples#> 1 <mot:m01_..> m01_GCCCTCTGSTGGC STREME-1 GCCMYCTGSTGGC DNA +- #> icscore nsites pval type pseudocount bkg best_match_name #> 1 15.22492 54 0.12 PCM 0 0.241, 0.... MA0139.2 -#> best_match_altname best_db_name -#> 1 CTCF c306429e5a3_JASPAR2024_CORE_non-redundant_pfms_meme.txt +#> best_match_altname best_db_name +#> 1 CTCF 78d116dfea_JASPAR2024_CORE_non-redundant_pfms_meme.txt #> best_match_offset best_match_pval best_match_eval best_match_qval #> 1 2 3.33e-13 7.81e-10 1.56e-09 #> best_match_strand best_match_motif tomtom @@ -158,8 +158,8 @@

Examples#> 1 <mot:m02_..> m02_GGAAGTAA STREME-2 GGAAGTAA DNA +- 10.9251 21 #> pval type pseudocount bkg best_match_name best_match_altname #> 1 0.5 PCM 0 0.241, 0.... MA1931.1 ELK1::HOXA1 -#> best_db_name best_match_offset -#> 1 c306429e5a3_JASPAR2024_CORE_non-redundant_pfms_meme.txt 3 +#> best_db_name best_match_offset +#> 1 78d116dfea_JASPAR2024_CORE_non-redundant_pfms_meme.txt 3 #> best_match_pval best_match_eval best_match_qval best_match_strand #> 1 1.55e-05 0.0365 0.0725 + #> best_match_motif tomtom diff --git a/reference/get_JASPARCORE.html b/reference/get_JASPARCORE.html index 7c8b508..33f97d3 100644 --- a/reference/get_JASPARCORE.html +++ b/reference/get_JASPARCORE.html @@ -70,8 +70,8 @@

Value

Examples

get_JASPARCORE()
-#>                                                                                          BFC1 
-#> "/github/home/.cache/R/BiocFileCache/c306429e5a3_JASPAR2024_CORE_non-redundant_pfms_meme.txt" 
+#>                                                                                         BFC1 
+#> "/github/home/.cache/R/BiocFileCache/78d116dfea_JASPAR2024_CORE_non-redundant_pfms_meme.txt"
diff --git a/reference/plot_enrichment_individual.html b/reference/plot_enrichment_individual.html index 90bf561..d96b86c 100644 --- a/reference/plot_enrichment_individual.html +++ b/reference/plot_enrichment_individual.html @@ -166,7 +166,7 @@

Examples print(plt) } #> <div class="plotly html-widget html-fill-item" id="htmlwidget-8a1f8f4a61c98a07d1d5" style="width:100%;height:400px;"></div> -#> <script type="application/json" data-for="htmlwidget-8a1f8f4a61c98a07d1d5">{"x":{"data":[{"orientation":"v","width":[0.89999999999999991,0.90000000000000013,0.90000000000000036,0.90000000000000036,0.90000000000000036,0.90000000000000036],"base":[66,50,48,49,15,3],"x":[1,2,3,4,5,6],"y":[34,70,79,78,67,54],"text":["<b>Peak Count:<\/b> 34 (68.42%)","<b>Peak Count:<\/b> 70 (72.53%)","<b>Peak Count:<\/b> 79 (62.2%)","<b>Peak Count:<\/b> 78 (61.42%)","<b>Peak Count:<\/b> 67 (81.71%)","<b>Peak Count:<\/b> 54 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","x"]},"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script> +#> <script type="application/json" data-for="htmlwidget-8a1f8f4a61c98a07d1d5">{"x":{"data":[{"orientation":"v","width":[0.89999999999999991,0.90000000000000013,0.90000000000000036,0.90000000000000036,0.90000000000000036,0.90000000000000036],"base":[66,50,48,49,15,3],"x":[1,2,3,4,5,6],"y":[34,70,79,78,67,54],"text":["<b>Peak Count:<\/b> 34 (68.42%)","<b>Peak Count:<\/b> 70 (72.53%)","<b>Peak Count:<\/b> 79 (62.2%)","<b>Peak Count:<\/b> 78 (61.42%)","<b>Peak Count:<\/b> 67 (81.71%)","<b>Peak Count:<\/b> 54 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","x"]},"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.20000000000000001,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script> diff --git a/reference/save_peak_file.html b/reference/save_peak_file.html index d527f61..3066b3e 100644 --- a/reference/save_peak_file.html +++ b/reference/save_peak_file.html @@ -100,7 +100,7 @@

Examples out <- save_peak_file(CTCF_ChIP_peaks, save = TRUE, "test_peak_file.bed") print(out) -#> [1] "/tmp/RtmpGJSeqg/test_peak_file.bed" +#> [1] "/tmp/RtmpzWRxoP/test_peak_file.bed" diff --git a/reference/to_plotly.html b/reference/to_plotly.html index 434e62a..a5b2abb 100644 --- a/reference/to_plotly.html +++ b/reference/to_plotly.html @@ -109,7 +109,7 @@

Examplesp <- ggplot2::ggplot(x, ggplot2::aes(x = a, y = b)) + ggplot2::geom_point() to_plotly(p, html_tags = FALSE)
- +