From b04ecaf9bf34897b03caa996c693f927df1d71dd Mon Sep 17 00:00:00 2001 From: HDash <16350928+HDash@users.noreply.github.com> Date: Mon, 2 Dec 2024 11:53:36 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20neurogen?= =?UTF-8?q?omics/MotifPeeker@9ad3396e778ac257a0d02cdac6de3626ca9280da=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 | 7 ++++--- index.html | 8 ++++---- pkgdown.yml | 2 +- reference/MotifPeeker.html | 2 +- reference/check_ENCODE.html | 2 +- reference/check_JASPAR.html | 2 +- reference/find_motifs.html | 4 ++-- reference/get_JASPARCORE.html | 4 ++-- reference/save_peak_file.html | 2 +- reference/to_plotly.html | 2 +- search.json | 2 +- 11 files changed, 19 insertions(+), 18 deletions(-) diff --git a/articles/MotifPeeker.html b/articles/MotifPeeker.html index a8f769a..b1dc458 100644 --- a/articles/MotifPeeker.html +++ b/articles/MotifPeeker.html @@ -178,6 +178,7 @@

Installation# Install latest version of MotifPeeker BiocManager::install("MotifPeeker", version = "devel", dependencies = TRUE) +# Load the package library(MotifPeeker)

Alternatively, you can use the Docker/Singularity container to run the package out-of-the-box.

@@ -292,9 +293,9 @@

Run MotifPeeker} 
## Starting run with 1 cores.
## Script run successfully. 
-## Output saved at: /tmp/RtmpC90tAD/MotifPeeker_20241202_111724 
-## Time taken: 1.04 mins.
-
## [1] "/tmp/RtmpC90tAD/MotifPeeker_20241202_111724"
+## Output saved at: /tmp/RtmpiNsPDN/MotifPeeker_20241202_115218 +## Time taken: 1.05 mins. +
## [1] "/tmp/RtmpiNsPDN/MotifPeeker_20241202_115218"

Required Inputs

diff --git a/index.html b/index.html index a5f4f86..97bd11c 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: Dec-02-2024

+

Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Maria Weinert, Nathan Skene
Updated: Dec-02-2024

Introduction

@@ -102,10 +102,10 @@

InstallationPerl dependency section of the MEME suite.

Once the MEME suite and its associated Perl dependencies are installed, the development version of MotifPeeker can be installed using the following code:

-if(!require("remotes")) install.packages("remotes")
+# Install latest version of MotifPeeker
+BiocManager::install("MotifPeeker", version = "devel", dependencies = TRUE)
 
-# Install latest version of MotifPeeker
-BiocManager::install("MotifPeeker", version = "devel", dependencies = TRUE) 
+# Load the package
 library(MotifPeeker)

Alternatively, you can use the Docker/Singularity container to run the package out-of-the-box.

diff --git a/pkgdown.yml b/pkgdown.yml index 1b1e0f6..7aee1d9 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: articles/examples: examples.html MotifPeeker: MotifPeeker.html troubleshooting: troubleshooting.html -last_built: 2024-12-02T11:15Z +last_built: 2024-12-02T11:50Z 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 e0cb537..02e7aab 100644 --- a/reference/MotifPeeker.html +++ b/reference/MotifPeeker.html @@ -331,7 +331,7 @@

Examples verbose = FALSE ) } -#> [1] "/tmp/Rtmp0g4LX4/MotifPeeker_20241202_111606" +#> [1] "/tmp/RtmpC7CHUq/MotifPeeker_20241202_115102" diff --git a/reference/check_ENCODE.html b/reference/check_ENCODE.html index c2ba1b8..9208527 100644 --- a/reference/check_ENCODE.html +++ b/reference/check_ENCODE.html @@ -83,7 +83,7 @@

Examples check_ENCODE("ENCFF920TXI", expect_format = c("bed", "gz")) } #> BFC2 -#> "/github/home/.cache/R/BiocFileCache/377b72759479_ENCFF920TXI.bed.gz" +#> "/github/home/.cache/R/BiocFileCache/10a4527ffc7b_ENCFF920TXI.bed.gz" diff --git a/reference/check_JASPAR.html b/reference/check_JASPAR.html index fd57296..3dcd780 100644 --- a/reference/check_JASPAR.html +++ b/reference/check_JASPAR.html @@ -74,7 +74,7 @@

Value

Examples

check_JASPAR("MA1930.2")
 #>                                                               BFC3 
-#> "/github/home/.cache/R/BiocFileCache/377b6822ed24_MA1930.2.jaspar" 
+#> "/github/home/.cache/R/BiocFileCache/10a44eee1763_MA1930.2.jaspar"
diff --git a/reference/find_motifs.html b/reference/find_motifs.html index b7db692..b8ab324 100644 --- a/reference/find_motifs.html +++ b/reference/find_motifs.html @@ -149,8 +149,8 @@

Examples#> 1 <mot:m01_..> m01_TCCCAGCACD STREME-1 TCCCAKMACN DNA +- 11.51542 #> nsites pval type pseudocount bkg best_match_name best_match_altname #> 1 21 1 PCM 0 0.24, 0..... MA2125.1 Zfp809 -#> best_db_name best_match_offset -#> 1 2ccd2bf270da_JASPAR2024_CORE_non-redundant_pfms_meme.txt 1 +#> best_db_name best_match_offset +#> 1 5c3585df44b_JASPAR2024_CORE_non-redundant_pfms_meme.txt 1 #> best_match_pval best_match_eval best_match_qval best_match_strand #> 1 3.6e-05 0.0845 0.169 + #> best_match_motif tomtom diff --git a/reference/get_JASPARCORE.html b/reference/get_JASPARCORE.html index e3a40ca..1e62650 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/2ccd2bf270da_JASPAR2024_CORE_non-redundant_pfms_meme.txt" 
+#>                                                                                          BFC1 
+#> "/github/home/.cache/R/BiocFileCache/5c3585df44b_JASPAR2024_CORE_non-redundant_pfms_meme.txt"
diff --git a/reference/save_peak_file.html b/reference/save_peak_file.html index e683b6b..499957a 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/Rtmp0g4LX4/test_peak_file.bed" +#> [1] "/tmp/RtmpC7CHUq/test_peak_file.bed" diff --git a/reference/to_plotly.html b/reference/to_plotly.html index 8476a10..0c275a7 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() MotifPeeker:::to_plotly(p, html_tags = FALSE)
- +