From 26adcd626232ee3104ab39465668f42d54458d61 Mon Sep 17 00:00:00 2001
From: js2264 <js2264@users.noreply.github.com>
Date: Wed, 15 Nov 2023 07:43:54 +0000
Subject: [PATCH] Built site for HiContactsData: 1.5.2@be3ede9

---
 404.html                      |  2 +-
 LICENSE-text.html             |  2 +-
 LICENSE.html                  |  2 +-
 articles/HiContactsData.html  | 20 ++++++++++----------
 articles/index.html           |  2 +-
 authors.html                  |  6 +++---
 index.html                    |  2 +-
 pkgdown.yml                   |  4 ++--
 reference/HiContactsData.html |  6 +++---
 reference/index.html          |  2 +-
 search.json                   |  2 +-
 11 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/404.html b/404.html
index 2a4a58d..ab252b1 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="http://jserizay.com/HiContactsData/index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index e9828ee..164927d 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 486189c..76160a3 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/HiContactsData.html b/articles/HiContactsData.html
index c64ce3b..a90ed72 100644
--- a/articles/HiContactsData.html
+++ b/articles/HiContactsData.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -69,7 +69,7 @@
                         <h4 data-toc-skip class="author">Jacques
 Serizay</h4>
             
-            <h4 data-toc-skip class="date">2023-11-07</h4>
+            <h4 data-toc-skip class="date">2023-11-15</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/js2264/HiContactsData/blob/HEAD/vignettes/HiContactsData.Rmd" class="external-link"><code>vignettes/HiContactsData.Rmd</code></a></small>
       <div class="d-none name"><code>HiContactsData.Rmd</code></div>
@@ -160,14 +160,14 @@ <h2 id="introduction-to-hicontactsdata">Introduction to HiContactsData<a class="
 <span><span class="co">#&gt; 12            only pairs from chrII are provided EH7705</span></span>
 <span><span class="co">#&gt; 13                         multi-res .mcool file EH7706</span></span>
 <span><span class="co">#&gt; 14            only pairs from chr13 are provided EH7707</span></span>
-<span><span class="co">#&gt; 15 multi-res .mcool file, only chr17 is provided</span></span>
+<span><span class="co">#&gt; 15 multi-res .mcool file, only chr17 is provided EH8535</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="va">cool_file</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/HiContactsData.html">HiContactsData</a></span><span class="op">(</span>sample <span class="op">=</span> <span class="st">'yeast_wt'</span>, format <span class="op">=</span> <span class="st">'cool'</span><span class="op">)</span></span>
 <span><span class="co">#&gt; see ?HiContactsData and browseVignettes('HiContactsData') for documentation</span></span>
 <span><span class="co">#&gt; loading from cache</span></span>
 <span><span class="va">cool_file</span></span>
-<span><span class="co">#&gt;                                                  EH7701 </span></span>
-<span><span class="co">#&gt; "/github/home/.cache/R/ExperimentHub/1c0c2b77d133_7751"</span></span></code></pre></div>
+<span><span class="co">#&gt;                                                 EH7701 </span></span>
+<span><span class="co">#&gt; "/github/home/.cache/R/ExperimentHub/c181bc9c5ac_7751"</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="hicontacts-and-hicontactsdata">HiContacts and HiContactsData<a class="anchor" aria-label="anchor" href="#hicontacts-and-hicontactsdata"></a>
@@ -182,7 +182,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 </h2>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span>
-<span><span class="co">#&gt; R Under development (unstable) (2023-11-02 r85465)</span></span>
+<span><span class="co">#&gt; R Under development (unstable) (2023-11-08 r85496)</span></span>
 <span><span class="co">#&gt; Platform: x86_64-pc-linux-gnu</span></span>
 <span><span class="co">#&gt; Running under: Ubuntu 22.04.3 LTS</span></span>
 <span><span class="co">#&gt; </span></span>
@@ -205,7 +205,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt; [1] HiContactsData_1.5.1 ExperimentHub_2.11.0 AnnotationHub_3.11.0</span></span>
+<span><span class="co">#&gt; [1] HiContactsData_1.5.2 ExperimentHub_2.11.0 AnnotationHub_3.11.0</span></span>
 <span><span class="co">#&gt; [4] BiocFileCache_2.11.1 dbplyr_2.4.0         BiocGenerics_0.49.1 </span></span>
 <span><span class="co">#&gt; [7] BiocStyle_2.31.0    </span></span>
 <span><span class="co">#&gt; </span></span>
@@ -220,9 +220,9 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [15] blob_1.2.4                    pkgconfig_2.0.3              </span></span>
 <span><span class="co">#&gt; [17] desc_1.4.2                    S4Vectors_0.41.1             </span></span>
 <span><span class="co">#&gt; [19] GenomeInfoDbData_1.2.11       lifecycle_1.0.4              </span></span>
-<span><span class="co">#&gt; [21] compiler_4.4.0                stringr_1.5.0                </span></span>
+<span><span class="co">#&gt; [21] compiler_4.4.0                stringr_1.5.1                </span></span>
 <span><span class="co">#&gt; [23] Biostrings_2.71.1             textshaping_0.3.7            </span></span>
-<span><span class="co">#&gt; [25] GenomeInfoDb_1.39.0           httpuv_1.6.12                </span></span>
+<span><span class="co">#&gt; [25] GenomeInfoDb_1.39.1           httpuv_1.6.12                </span></span>
 <span><span class="co">#&gt; [27] htmltools_0.5.7               sass_0.4.7                   </span></span>
 <span><span class="co">#&gt; [29] RCurl_1.98-1.13               yaml_2.3.7                   </span></span>
 <span><span class="co">#&gt; [31] interactiveDisplayBase_1.41.0 crayon_1.5.2                 </span></span>
@@ -230,7 +230,7 @@ <h2 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#s
 <span><span class="co">#&gt; [35] later_1.3.1                   jquerylib_0.1.4              </span></span>
 <span><span class="co">#&gt; [37] ellipsis_0.3.2                cachem_1.0.8                 </span></span>
 <span><span class="co">#&gt; [39] mime_0.12                     tidyselect_1.2.0             </span></span>
-<span><span class="co">#&gt; [41] digest_0.6.33                 stringi_1.7.12               </span></span>
+<span><span class="co">#&gt; [41] digest_0.6.33                 stringi_1.8.1                </span></span>
 <span><span class="co">#&gt; [43] dplyr_1.1.3                   purrr_1.0.2                  </span></span>
 <span><span class="co">#&gt; [45] bookdown_0.36                 BiocVersion_3.19.1           </span></span>
 <span><span class="co">#&gt; [47] rprojroot_2.0.4               fastmap_1.1.1                </span></span>
diff --git a/articles/index.html b/articles/index.html
index 0dac5a2..1ecc365 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index 427fb00..51af0ae 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -58,13 +58,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Serizay J (2023).
 <em>HiContactsData: HiContacts companion data package</em>.
-R package version 1.5.1, <a href="https://github.com/js2264/HiContactsData" class="external-link">https://github.com/js2264/HiContactsData</a>. 
+R package version 1.5.2, <a href="https://github.com/js2264/HiContactsData" class="external-link">https://github.com/js2264/HiContactsData</a>. 
 </p>
       <pre>@Manual{,
   title = {HiContactsData: HiContacts companion data package},
   author = {Jacques Serizay},
   year = {2023},
-  note = {R package version 1.5.1},
+  note = {R package version 1.5.2},
   url = {https://github.com/js2264/HiContactsData},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 329790a..5114fea 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index 51d5d68..803c9d1 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,9 @@
 pandoc: 3.1.1
 pkgdown: 2.0.7.9000
-pkgdown_sha: ab96d2fa60be7a6e54eb8132b572688eadc41be3
+pkgdown_sha: 5a0a31f89d7c839c04a929844e4b7216196189ca
 articles:
   HiContactsData: HiContactsData.html
-last_built: 2023-11-07T19:06Z
+last_built: 2023-11-15T07:43Z
 urls:
   reference: http://jserizay.com/HiContactsData/reference
   article: http://jserizay.com/HiContactsData/articles
diff --git a/reference/HiContactsData.html b/reference/HiContactsData.html
index 9a9f5ba..8db1add 100644
--- a/reference/HiContactsData.html
+++ b/reference/HiContactsData.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -79,8 +79,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">HiContactsData</span><span class="op">(</span>sample <span class="op">=</span> <span class="st">'yeast_wt'</span>, format <span class="op">=</span> <span class="st">'cool'</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> see ?HiContactsData and browseVignettes('HiContactsData') for documentation</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> loading from cache</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>                                                  EH7701 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> "/github/home/.cache/R/ExperimentHub/1c0c2b77d133_7751" </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>                                                 EH7701 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> "/github/home/.cache/R/ExperimentHub/c181bc9c5ac_7751" </span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/index.html b/reference/index.html
index 6a4fd2c..d8d6f7f 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">HiContactsData</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 29a3827..96e127e 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"http://jserizay.com/HiContactsData/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 Jacques Serizay Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://jserizay.com/HiContactsData/articles/HiContactsData.html","id":"introduction-to-hicontactsdata","dir":"Articles","previous_headings":"","what":"Introduction to HiContactsData","title":"HiContactsData","text":"HiContactsData companion data package giving programmatic access several processed Hi-C files demonstration, cool, mcool pairs files. meant used HiContacts. function provided HiContactsData package HiContactsData(). Several files avaible using function, namely: S288C fastq files (R1 & R2) (sample: yeast_wt, format = fastq_R{12}) S288C HiCool processing log (sample: yeast_wt, format = HiCool_log) S288C.cool (sample: yeast_wt, format = cool) S288C.mcool (sample: yeast_wt, format = mcool) S288C.hic (sample: yeast_wt, format = hic) S288C.hicpro.matrix (sample: yeast_wt, format = hicpro_matrix) S288C.hicpro.bed (sample: yeast_wt, format = hicpro_bed) S288C.pairs.gz chrII (sample: yeast_wt, format = pairs) S288C_Eco1-AID.mcool (sample: yeast_Eco1, format = mcool) S288C_Eco1-AID.pairs.gz chrII (sample: yeast_Eco1, format = pairs) mESCs.mcool (sample: mESCs, format = mcool) mESCs.pairs.gz chr13 (sample: mESCs, format = pairs) microC_HFFc6_chr17.mcool (sample: microC, format = mcool) Yeast data comes Bastie, Chapard et al., Nature Structural & Molecular Biology 2022 mouse ESC data comes Bonev et al., Cell 2017. Human HcFF6 micro-C data comes Krietenstein et al., Mol. Cell 2020. download one files, one can specify sample file format:","code":"library(HiContactsData) cool_file <- HiContactsData() #> Available files: #>        sample        format genome    condition #> 1    yeast_wt      fastq_R1  S288C    wild-type #> 2    yeast_wt      fastq_R2  S288C    wild-type #> 3    yeast_wt    HiCool_log  S288C    wild-type #> 4    yeast_wt      pairs.gz  S288C    wild-type #> 5    yeast_wt          cool  S288C    wild-type #> 6    yeast_wt         mcool  S288C    wild-type #> 7    yeast_wt           hic  S288C    wild-type #> 8    yeast_wt hicpro_matrix  S288C    wild-type #> 9    yeast_wt    hicpro_bed  S288C    wild-type #> 10   yeast_wt  hicpro_pairs  S288C    wild-type #> 11 yeast_eco1         mcool  S288C Eco1-AID+IAA #> 12 yeast_eco1      pairs.gz  S288C Eco1-AID+IAA #> 13      mESCs         mcool   mm10        mESCs #> 14      mESCs      pairs.gz   mm10        mESCs #> 15     microC         mcool GRCh38        HFFc6 #>                                            notes   EHID #> 1                                     fastq (R1) EH7783 #> 2                                     fastq (R2) EH7784 #> 3                                HiCool log file EH7785 #> 4             only pairs from chrII are provided EH7703 #> 5                 .cool file @ resolution of 1kb EH7701 #> 6                          multi-res .mcool file EH7702 #> 7                            multi-res .hic file EH7786 #> 8                      HiC-Pro matrix file @ 1kb EH7787 #> 9                         HiC-Pro bed file @ 1kb EH7788 #> 10                   HiC-Pro .allValidPairs file EH7789 #> 11                         multi-res .mcool file EH7704 #> 12            only pairs from chrII are provided EH7705 #> 13                         multi-res .mcool file EH7706 #> 14            only pairs from chr13 are provided EH7707 #> 15 multi-res .mcool file, only chr17 is provided #>  cool_file <- HiContactsData(sample = 'yeast_wt', format = 'cool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache cool_file #>                                                  EH7701  #> \"/github/home/.cache/R/ExperimentHub/1c0c2b77d133_7751\""},{"path":"http://jserizay.com/HiContactsData/articles/HiContactsData.html","id":"hicontacts-and-hicontactsdata","dir":"Articles","previous_headings":"","what":"HiContacts and HiContactsData","title":"HiContactsData","text":"HiCExperiment package can used import data provided HiContactsData. Refer HiCExperiment package documentation information.","code":""},{"path":"http://jserizay.com/HiContactsData/articles/HiContactsData.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"HiContactsData","text":"","code":"sessionInfo() #> R Under development (unstable) (2023-11-02 r85465) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] HiContactsData_1.5.1 ExperimentHub_2.11.0 AnnotationHub_3.11.0 #> [4] BiocFileCache_2.11.1 dbplyr_2.4.0         BiocGenerics_0.49.1  #> [7] BiocStyle_2.31.0     #>  #> loaded via a namespace (and not attached): #>  [1] KEGGREST_1.43.0               xfun_0.41                     #>  [3] bslib_0.5.1                   Biobase_2.63.0                #>  [5] bitops_1.0-7                  vctrs_0.6.4                   #>  [7] tools_4.4.0                   generics_0.1.3                #>  [9] stats4_4.4.0                  curl_5.1.0                    #> [11] AnnotationDbi_1.65.2          tibble_3.2.1                  #> [13] fansi_1.0.5                   RSQLite_2.3.3                 #> [15] blob_1.2.4                    pkgconfig_2.0.3               #> [17] desc_1.4.2                    S4Vectors_0.41.1              #> [19] GenomeInfoDbData_1.2.11       lifecycle_1.0.4               #> [21] compiler_4.4.0                stringr_1.5.0                 #> [23] Biostrings_2.71.1             textshaping_0.3.7             #> [25] GenomeInfoDb_1.39.0           httpuv_1.6.12                 #> [27] htmltools_0.5.7               sass_0.4.7                    #> [29] RCurl_1.98-1.13               yaml_2.3.7                    #> [31] interactiveDisplayBase_1.41.0 crayon_1.5.2                  #> [33] pillar_1.9.0                  pkgdown_2.0.7.9000            #> [35] later_1.3.1                   jquerylib_0.1.4               #> [37] ellipsis_0.3.2                cachem_1.0.8                  #> [39] mime_0.12                     tidyselect_1.2.0              #> [41] digest_0.6.33                 stringi_1.7.12                #> [43] dplyr_1.1.3                   purrr_1.0.2                   #> [45] bookdown_0.36                 BiocVersion_3.19.1            #> [47] rprojroot_2.0.4               fastmap_1.1.1                 #> [49] cli_3.6.1                     magrittr_2.0.3                #> [51] utf8_1.2.4                    withr_2.5.2                   #> [53] filelock_1.0.2                promises_1.2.1                #> [55] rappdirs_0.3.3                bit64_4.0.5                   #> [57] XVector_0.43.0                rmarkdown_2.25                #> [59] httr_1.4.7                    bit_4.0.5                     #> [61] png_0.1-8                     ragg_1.2.6                    #> [63] memoise_2.0.1                 shiny_1.7.5.1                 #> [65] evaluate_0.23                 knitr_1.45                    #> [67] IRanges_2.37.0                rlang_1.1.2                   #> [69] Rcpp_1.0.11                   xtable_1.8-4                  #> [71] glue_1.6.2                    DBI_1.1.3                     #> [73] BiocManager_1.30.22           jsonlite_1.8.7                #> [75] R6_2.5.1                      zlibbioc_1.49.0               #> [77] systemfonts_1.0.5             fs_1.6.3"},{"path":"http://jserizay.com/HiContactsData/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jacques Serizay. Author, maintainer.","code":""},{"path":"http://jserizay.com/HiContactsData/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Serizay J (2023). HiContactsData: HiContacts companion data package. R package version 1.5.1, https://github.com/js2264/HiContactsData.","code":"@Manual{,   title = {HiContactsData: HiContacts companion data package},   author = {Jacques Serizay},   year = {2023},   note = {R package version 1.5.1},   url = {https://github.com/js2264/HiContactsData}, }"},{"path":"http://jserizay.com/HiContactsData/index.html","id":"hicontactsdata","dir":"","previous_headings":"","what":"HiContacts companion data package","title":"HiContacts companion data package","text":"HiContactsData companion data package giving programmatic access several processed Hi-C files demonstration, cool, mcool pairs files. meant used HiContacts. function provided HiContactsData package HiContactsData(). Several files avaible using function, namely: S288C fastq files (R1 & R2) (sample: yeast_wt, format = fastq_R{12}) S288C HiCool processing log (sample: yeast_wt, format = HiCool_log) S288C.cool (sample: yeast_wt, format = cool) S288C.mcool (sample: yeast_wt, format = mcool) S288C.hic (sample: yeast_wt, format = hic) S288C.hicpro.matrix (sample: yeast_wt, format = hicpro_matrix) S288C.hicpro.bed (sample: yeast_wt, format = hicpro_bed) S288C.pairs.gz chrII (sample: yeast_wt, format = pairs) S288C_Eco1-AID.mcool (sample: yeast_Eco1, format = mcool) S288C_Eco1-AID.pairs.gz chrII (sample: yeast_Eco1, format = pairs) mESCs.mcool (sample: mESCs, format = mcool) mESCs.pairs.gz chr13 (sample: mESCs, format = pairs) microC_HFFc6_chr17.mcool (sample: microC, format = mcool)","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":null,"dir":"Reference","previous_headings":"","what":"HiContactsData — HiContactsData","title":"HiContactsData — HiContactsData","text":"Downloads different types Hi-C processed files (cool, mcool, pairs.gz, fastq) returns path cached file.","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HiContactsData — HiContactsData","text":"","code":"HiContactsData(sample = NULL, format = NULL)"},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"HiContactsData — HiContactsData","text":"sample sample format format","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"HiContactsData — HiContactsData","text":"Local path queried file cached BiocFileCache.","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"HiContactsData — HiContactsData","text":"","code":"HiContactsData(sample = 'yeast_wt', format = 'cool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache #>                                                  EH7701  #> \"/github/home/.cache/R/ExperimentHub/1c0c2b77d133_7751\""}]
+[{"path":"http://jserizay.com/HiContactsData/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 Jacques Serizay Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://jserizay.com/HiContactsData/articles/HiContactsData.html","id":"introduction-to-hicontactsdata","dir":"Articles","previous_headings":"","what":"Introduction to HiContactsData","title":"HiContactsData","text":"HiContactsData companion data package giving programmatic access several processed Hi-C files demonstration, cool, mcool pairs files. meant used HiContacts. function provided HiContactsData package HiContactsData(). Several files avaible using function, namely: S288C fastq files (R1 & R2) (sample: yeast_wt, format = fastq_R{12}) S288C HiCool processing log (sample: yeast_wt, format = HiCool_log) S288C.cool (sample: yeast_wt, format = cool) S288C.mcool (sample: yeast_wt, format = mcool) S288C.hic (sample: yeast_wt, format = hic) S288C.hicpro.matrix (sample: yeast_wt, format = hicpro_matrix) S288C.hicpro.bed (sample: yeast_wt, format = hicpro_bed) S288C.pairs.gz chrII (sample: yeast_wt, format = pairs) S288C_Eco1-AID.mcool (sample: yeast_Eco1, format = mcool) S288C_Eco1-AID.pairs.gz chrII (sample: yeast_Eco1, format = pairs) mESCs.mcool (sample: mESCs, format = mcool) mESCs.pairs.gz chr13 (sample: mESCs, format = pairs) microC_HFFc6_chr17.mcool (sample: microC, format = mcool) Yeast data comes Bastie, Chapard et al., Nature Structural & Molecular Biology 2022 mouse ESC data comes Bonev et al., Cell 2017. Human HcFF6 micro-C data comes Krietenstein et al., Mol. Cell 2020. download one files, one can specify sample file format:","code":"library(HiContactsData) cool_file <- HiContactsData() #> Available files: #>        sample        format genome    condition #> 1    yeast_wt      fastq_R1  S288C    wild-type #> 2    yeast_wt      fastq_R2  S288C    wild-type #> 3    yeast_wt    HiCool_log  S288C    wild-type #> 4    yeast_wt      pairs.gz  S288C    wild-type #> 5    yeast_wt          cool  S288C    wild-type #> 6    yeast_wt         mcool  S288C    wild-type #> 7    yeast_wt           hic  S288C    wild-type #> 8    yeast_wt hicpro_matrix  S288C    wild-type #> 9    yeast_wt    hicpro_bed  S288C    wild-type #> 10   yeast_wt  hicpro_pairs  S288C    wild-type #> 11 yeast_eco1         mcool  S288C Eco1-AID+IAA #> 12 yeast_eco1      pairs.gz  S288C Eco1-AID+IAA #> 13      mESCs         mcool   mm10        mESCs #> 14      mESCs      pairs.gz   mm10        mESCs #> 15     microC         mcool GRCh38        HFFc6 #>                                            notes   EHID #> 1                                     fastq (R1) EH7783 #> 2                                     fastq (R2) EH7784 #> 3                                HiCool log file EH7785 #> 4             only pairs from chrII are provided EH7703 #> 5                 .cool file @ resolution of 1kb EH7701 #> 6                          multi-res .mcool file EH7702 #> 7                            multi-res .hic file EH7786 #> 8                      HiC-Pro matrix file @ 1kb EH7787 #> 9                         HiC-Pro bed file @ 1kb EH7788 #> 10                   HiC-Pro .allValidPairs file EH7789 #> 11                         multi-res .mcool file EH7704 #> 12            only pairs from chrII are provided EH7705 #> 13                         multi-res .mcool file EH7706 #> 14            only pairs from chr13 are provided EH7707 #> 15 multi-res .mcool file, only chr17 is provided EH8535 #>  cool_file <- HiContactsData(sample = 'yeast_wt', format = 'cool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache cool_file #>                                                 EH7701  #> \"/github/home/.cache/R/ExperimentHub/c181bc9c5ac_7751\""},{"path":"http://jserizay.com/HiContactsData/articles/HiContactsData.html","id":"hicontacts-and-hicontactsdata","dir":"Articles","previous_headings":"","what":"HiContacts and HiContactsData","title":"HiContactsData","text":"HiCExperiment package can used import data provided HiContactsData. Refer HiCExperiment package documentation information.","code":""},{"path":"http://jserizay.com/HiContactsData/articles/HiContactsData.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"HiContactsData","text":"","code":"sessionInfo() #> R Under development (unstable) (2023-11-08 r85496) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] HiContactsData_1.5.2 ExperimentHub_2.11.0 AnnotationHub_3.11.0 #> [4] BiocFileCache_2.11.1 dbplyr_2.4.0         BiocGenerics_0.49.1  #> [7] BiocStyle_2.31.0     #>  #> loaded via a namespace (and not attached): #>  [1] KEGGREST_1.43.0               xfun_0.41                     #>  [3] bslib_0.5.1                   Biobase_2.63.0                #>  [5] bitops_1.0-7                  vctrs_0.6.4                   #>  [7] tools_4.4.0                   generics_0.1.3                #>  [9] stats4_4.4.0                  curl_5.1.0                    #> [11] AnnotationDbi_1.65.2          tibble_3.2.1                  #> [13] fansi_1.0.5                   RSQLite_2.3.3                 #> [15] blob_1.2.4                    pkgconfig_2.0.3               #> [17] desc_1.4.2                    S4Vectors_0.41.1              #> [19] GenomeInfoDbData_1.2.11       lifecycle_1.0.4               #> [21] compiler_4.4.0                stringr_1.5.1                 #> [23] Biostrings_2.71.1             textshaping_0.3.7             #> [25] GenomeInfoDb_1.39.1           httpuv_1.6.12                 #> [27] htmltools_0.5.7               sass_0.4.7                    #> [29] RCurl_1.98-1.13               yaml_2.3.7                    #> [31] interactiveDisplayBase_1.41.0 crayon_1.5.2                  #> [33] pillar_1.9.0                  pkgdown_2.0.7.9000            #> [35] later_1.3.1                   jquerylib_0.1.4               #> [37] ellipsis_0.3.2                cachem_1.0.8                  #> [39] mime_0.12                     tidyselect_1.2.0              #> [41] digest_0.6.33                 stringi_1.8.1                 #> [43] dplyr_1.1.3                   purrr_1.0.2                   #> [45] bookdown_0.36                 BiocVersion_3.19.1            #> [47] rprojroot_2.0.4               fastmap_1.1.1                 #> [49] cli_3.6.1                     magrittr_2.0.3                #> [51] utf8_1.2.4                    withr_2.5.2                   #> [53] filelock_1.0.2                promises_1.2.1                #> [55] rappdirs_0.3.3                bit64_4.0.5                   #> [57] XVector_0.43.0                rmarkdown_2.25                #> [59] httr_1.4.7                    bit_4.0.5                     #> [61] png_0.1-8                     ragg_1.2.6                    #> [63] memoise_2.0.1                 shiny_1.7.5.1                 #> [65] evaluate_0.23                 knitr_1.45                    #> [67] IRanges_2.37.0                rlang_1.1.2                   #> [69] Rcpp_1.0.11                   xtable_1.8-4                  #> [71] glue_1.6.2                    DBI_1.1.3                     #> [73] BiocManager_1.30.22           jsonlite_1.8.7                #> [75] R6_2.5.1                      zlibbioc_1.49.0               #> [77] systemfonts_1.0.5             fs_1.6.3"},{"path":"http://jserizay.com/HiContactsData/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jacques Serizay. Author, maintainer.","code":""},{"path":"http://jserizay.com/HiContactsData/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Serizay J (2023). HiContactsData: HiContacts companion data package. R package version 1.5.2, https://github.com/js2264/HiContactsData.","code":"@Manual{,   title = {HiContactsData: HiContacts companion data package},   author = {Jacques Serizay},   year = {2023},   note = {R package version 1.5.2},   url = {https://github.com/js2264/HiContactsData}, }"},{"path":"http://jserizay.com/HiContactsData/index.html","id":"hicontactsdata","dir":"","previous_headings":"","what":"HiContacts companion data package","title":"HiContacts companion data package","text":"HiContactsData companion data package giving programmatic access several processed Hi-C files demonstration, cool, mcool pairs files. meant used HiContacts. function provided HiContactsData package HiContactsData(). Several files avaible using function, namely: S288C fastq files (R1 & R2) (sample: yeast_wt, format = fastq_R{12}) S288C HiCool processing log (sample: yeast_wt, format = HiCool_log) S288C.cool (sample: yeast_wt, format = cool) S288C.mcool (sample: yeast_wt, format = mcool) S288C.hic (sample: yeast_wt, format = hic) S288C.hicpro.matrix (sample: yeast_wt, format = hicpro_matrix) S288C.hicpro.bed (sample: yeast_wt, format = hicpro_bed) S288C.pairs.gz chrII (sample: yeast_wt, format = pairs) S288C_Eco1-AID.mcool (sample: yeast_Eco1, format = mcool) S288C_Eco1-AID.pairs.gz chrII (sample: yeast_Eco1, format = pairs) mESCs.mcool (sample: mESCs, format = mcool) mESCs.pairs.gz chr13 (sample: mESCs, format = pairs) microC_HFFc6_chr17.mcool (sample: microC, format = mcool)","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":null,"dir":"Reference","previous_headings":"","what":"HiContactsData — HiContactsData","title":"HiContactsData — HiContactsData","text":"Downloads different types Hi-C processed files (cool, mcool, pairs.gz, fastq) returns path cached file.","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"HiContactsData — HiContactsData","text":"","code":"HiContactsData(sample = NULL, format = NULL)"},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"HiContactsData — HiContactsData","text":"sample sample format format","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"HiContactsData — HiContactsData","text":"Local path queried file cached BiocFileCache.","code":""},{"path":"http://jserizay.com/HiContactsData/reference/HiContactsData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"HiContactsData — HiContactsData","text":"","code":"HiContactsData(sample = 'yeast_wt', format = 'cool') #> see ?HiContactsData and browseVignettes('HiContactsData') for documentation #> loading from cache #>                                                 EH7701  #> \"/github/home/.cache/R/ExperimentHub/c181bc9c5ac_7751\""}]