From 12f2de5f9c8e3c736819681e9a890577c9d7b1af Mon Sep 17 00:00:00 2001
From: lpantano <lorena.pantano@gmail.com>
Date: Tue, 18 Jun 2024 14:43:50 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bcbio/bc?=
 =?UTF-8?q?bioR@d9df05400ff6b17fc10261eb82504837fdf558fd=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                               |  2 +-
 LICENSE-text.html                      |  2 +-
 LICENSE.html                           |  2 +-
 articles/bcbioR_quick_start.html       | 60 +++++++++++++-------------
 articles/index.html                    |  2 +-
 authors.html                           |  6 +--
 index.html                             |  2 +-
 news/index.html                        |  7 +--
 pkgdown.yml                            |  2 +-
 reference/bcbioR-package.html          |  2 +-
 reference/bcbio_nfcore_check.html      |  2 +-
 reference/bcbio_set_project.html       |  2 +-
 reference/bcbio_templates.html         |  2 +-
 reference/bcbio_vsd_data.html          |  2 +-
 reference/cb_friendly_colors.html      |  2 +-
 reference/cb_friendly_cols.html        |  2 +-
 reference/cb_friendly_pal.html         |  2 +-
 reference/cb_friendly_palettes.html    |  2 +-
 reference/index.html                   |  2 +-
 reference/list_cb_friendly_cols.html   |  2 +-
 reference/scale_color_cb_friendly.html |  2 +-
 reference/scale_fill_cb_friendly.html  |  2 +-
 search.json                            |  2 +-
 23 files changed, 57 insertions(+), 56 deletions(-)

diff --git a/404.html b/404.html
index 875f1d8..7193a2f 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="http://bcb.io/bcbioR/index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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 c398ec7..022e8dc 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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 47ba837..09cb1ba 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/bcbioR_quick_start.html b/articles/bcbioR_quick_start.html
index abbb2a4..0070adc 100644
--- a/articles/bcbioR_quick_start.html
+++ b/articles/bcbioR_quick_start.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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">
@@ -115,17 +115,17 @@ <h2 id="set-projects">Set projects<a class="anchor" aria-label="anchor" href="#s
 <code class="sourceCode R"><span><span class="va">tmp_dir</span><span class="op">=</span><span class="fu">withr</span><span class="fu">::</span><span class="fu"><a href="https://withr.r-lib.org/reference/with_tempfile.html" class="external-link">local_tempdir</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/bcbio_templates.html">bcbio_templates</a></span><span class="op">(</span>type<span class="op">=</span><span class="st">"base"</span>, outpath<span class="op">=</span><span class="va">tmp_dir</span><span class="op">)</span></span>
 <span><span class="fu">fs</span><span class="fu">::</span><span class="fu"><a href="https://fs.r-lib.org/reference/dir_ls.html" class="external-link">dir_ls</a></span><span class="op">(</span><span class="va">tmp_dir</span>, recurse<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; /tmp/RtmpI7h5tU/file233c25d2e7a8/README.md</span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmpI7h5tU/file233c25d2e7a8/code</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/code/placeholder.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmpI7h5tU/file233c25d2e7a8/data</span></span></span>
-<span><span class="co">#&gt; /tmp/RtmpI7h5tU/file233c25d2e7a8/data/readme</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/information.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmpI7h5tU/file233c25d2e7a8/meta</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/meta/placeholder.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmpI7h5tU/file233c25d2e7a8/scripts</span></span></span>
-<span><span class="co">#&gt; /tmp/RtmpI7h5tU/file233c25d2e7a8/scripts/placeholder</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/skeleton.Rmd</span></span></span></code></pre></div>
+<span><span class="co">#&gt; /tmp/RtmphGxu3P/file22a383ac3fe/README.md</span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmphGxu3P/file22a383ac3fe/code</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/code/placeholder.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmphGxu3P/file22a383ac3fe/data</span></span></span>
+<span><span class="co">#&gt; /tmp/RtmphGxu3P/file22a383ac3fe/data/readme</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/information.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmphGxu3P/file22a383ac3fe/meta</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/meta/placeholder.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmphGxu3P/file22a383ac3fe/scripts</span></span></span>
+<span><span class="co">#&gt; /tmp/RtmphGxu3P/file22a383ac3fe/scripts/placeholder</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/skeleton.Rmd</span></span></span></code></pre></div>
 <p>We support multiple analyses type:</p>
 <ul>
 <li>RNAseq</li>
@@ -139,24 +139,24 @@ <h2 id="set-projects">Set projects<a class="anchor" aria-label="anchor" href="#s
 <code class="sourceCode R"><span><span class="va">analysis_tmp</span><span class="op">=</span><span class="fu">fs</span><span class="fu">::</span><span class="fu"><a href="https://fs.r-lib.org/reference/path_math.html" class="external-link">path_join</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">tmp_dir</span>, <span class="st">"reports"</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../reference/bcbio_templates.html">bcbio_templates</a></span><span class="op">(</span>type<span class="op">=</span><span class="st">"rnaseq"</span>, outpath<span class="op">=</span><span class="va">analysis_tmp</span><span class="op">)</span></span>
 <span><span class="fu">fs</span><span class="fu">::</span><span class="fu"><a href="https://fs.r-lib.org/reference/dir_ls.html" class="external-link">dir_ls</a></span><span class="op">(</span><span class="va">analysis_tmp</span>, recurse<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/DEG.Rmd</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/PCA_variance_analysis.Rmd</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/load_data.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/params_de-example.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/params_de.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/run_markdown.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/QC.Rmd</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/QC_nf-core.Rmd</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/params_qc.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/params_qc_nf-core-example.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/params_qc_nf-core.R</span></span></span>
-<span><span class="co">#&gt; /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/placeholder</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/run_markdown.R</span></span></span>
-<span><span class="co">#&gt; /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/README.md</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/information.R</span></span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmpI7h5tU/file233c25d2e7a8/reports/skeleton.Rmd</span></span></span></code></pre></div>
+<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/DE</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/DEG.Rmd</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/PCA_variance_analysis.Rmd</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/load_data.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/params_de-example.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/params_de.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/run_markdown.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB; font-weight: bold;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/QC</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/QC.Rmd</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/QC_nf-core.Rmd</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/params_qc.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/params_qc_nf-core-example.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/params_qc_nf-core.R</span></span></span>
+<span><span class="co">#&gt; /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/placeholder</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/run_markdown.R</span></span></span>
+<span><span class="co">#&gt; /tmp/RtmphGxu3P/file22a383ac3fe/reports/README.md</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/information.R</span></span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">/tmp/RtmphGxu3P/file22a383ac3fe/reports/skeleton.Rmd</span></span></span></code></pre></div>
 <p>Use <code>scrnaseq</code>, <code>teaseq</code> or <code>cosmx</code>
 to get those other templates.</p>
 </div>
diff --git a/articles/index.html b/articles/index.html
index 9e52a6d..b0b97f4 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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 fa36446..371e0fc 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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>Lorena P (2024).
 <em>bcbioR: Templates and functions to guide downstream analysis and data interpretation</em>.
-R package version 0.1.2, <a href="http://bcb.io/bcbioR/">http://bcb.io/bcbioR/</a>. 
+R package version 0.1.3, <a href="http://bcb.io/bcbioR/">http://bcb.io/bcbioR/</a>. 
 </p>
       <pre>@Manual{,
   title = {bcbioR: Templates and functions to guide downstream analysis and data interpretation},
   author = {Pantano Lorena},
   year = {2024},
-  note = {R package version 0.1.2},
+  note = {R package version 0.1.3},
   url = {http://bcb.io/bcbioR/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index a40d7b3..7630ca1 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/news/index.html b/news/index.html
index 641f65a..f78fcfd 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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">
@@ -45,8 +45,9 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.1.2" id="bcbior-012">bcbioR 0.1.2<a class="anchor" aria-label="anchor" href="#bcbior-012"></a></h2>
-<ul><li>Add draft templates for TEAseq, COSMX</li>
+<h2 class="pkg-version" data-toc-text="0.1.3" id="bcbior-013">bcbioR 0.1.3<a class="anchor" aria-label="anchor" href="#bcbior-013"></a></h2>
+<ul><li>Add combatseq</li>
+<li>Add draft templates for TEAseq, COSMX</li>
 <li>Adapt templates to nf-core rnaseq</li>
 <li>Fix when sample start by number</li>
 <li>Fix when rRNA rate is missing</li>
diff --git a/pkgdown.yml b/pkgdown.yml
index 65a493b..e5946c6 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   bcbioR_quick_start: bcbioR_quick_start.html
-last_built: 2024-06-05T22:43Z
+last_built: 2024-06-18T14:43Z
 urls:
   reference: http://bcb.io/bcbioR/reference
   article: http://bcb.io/bcbioR/articles
diff --git a/reference/bcbioR-package.html b/reference/bcbioR-package.html
index 6a2ea0c..ac8d19b 100644
--- a/reference/bcbioR-package.html
+++ b/reference/bcbioR-package.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/bcbio_nfcore_check.html b/reference/bcbio_nfcore_check.html
index 128b076..e453f45 100644
--- a/reference/bcbio_nfcore_check.html
+++ b/reference/bcbio_nfcore_check.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/bcbio_set_project.html b/reference/bcbio_set_project.html
index fdc972d..63b42c7 100644
--- a/reference/bcbio_set_project.html
+++ b/reference/bcbio_set_project.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/bcbio_templates.html b/reference/bcbio_templates.html
index 9280801..78d9cf2 100644
--- a/reference/bcbio_templates.html
+++ b/reference/bcbio_templates.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/bcbio_vsd_data.html b/reference/bcbio_vsd_data.html
index 9f55ee8..80a9be7 100644
--- a/reference/bcbio_vsd_data.html
+++ b/reference/bcbio_vsd_data.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/cb_friendly_colors.html b/reference/cb_friendly_colors.html
index b2da3a2..3f365f3 100644
--- a/reference/cb_friendly_colors.html
+++ b/reference/cb_friendly_colors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/cb_friendly_cols.html b/reference/cb_friendly_cols.html
index 74007fe..75c2606 100644
--- a/reference/cb_friendly_cols.html
+++ b/reference/cb_friendly_cols.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/cb_friendly_pal.html b/reference/cb_friendly_pal.html
index d9bc0a5..d1b287f 100644
--- a/reference/cb_friendly_pal.html
+++ b/reference/cb_friendly_pal.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/cb_friendly_palettes.html b/reference/cb_friendly_palettes.html
index e8f8835..41af1b6 100644
--- a/reference/cb_friendly_palettes.html
+++ b/reference/cb_friendly_palettes.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/index.html b/reference/index.html
index abd4398..a3c36af 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/list_cb_friendly_cols.html b/reference/list_cb_friendly_cols.html
index 7d06df5..eefe3a3 100644
--- a/reference/list_cb_friendly_cols.html
+++ b/reference/list_cb_friendly_cols.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/scale_color_cb_friendly.html b/reference/scale_color_cb_friendly.html
index 9b9297c..a72de6e 100644
--- a/reference/scale_color_cb_friendly.html
+++ b/reference/scale_color_cb_friendly.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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/reference/scale_fill_cb_friendly.html b/reference/scale_fill_cb_friendly.html
index 92f804b..1f22296 100644
--- a/reference/scale_fill_cb_friendly.html
+++ b/reference/scale_fill_cb_friendly.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">bcbioR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.3</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 4643623..113eca7 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"http://bcb.io/bcbioR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 bcbioR authors 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://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"color-blind-friendly-palette","dir":"Articles","previous_headings":"","what":"Color blind friendly palette","title":"bcbioR quick start","text":"Compatible ggplot.  get colors directly: full palette:","code":"set.seed(596) dsamp <- diamonds[sample(nrow(diamonds), 1000), ] ggplot(dsamp, aes(carat, price)) +   geom_point(aes(colour = clarity)) +   scale_color_cb_friendly() cb_friendly_cols(1:16) #>         blue light_orange  olive_green       purple         pink     sky_blue  #>    \"#2759F6\"    \"#FFD37D\" \"olivedrab3\"    \"#9176C8\"    \"#E93380\"    \"#4FAEEB\"  #>    blue_grey forest_green       yellow  dark_purple  dark_orange   army_green  #>    \"#92A6BC\"    \"#3C877B\"     \"yellow\"    \"#402999\"    \"#D5392C\"    \"#C3C380\"  #>        black    dark_grey   light_blue        brown  #>      \"black\"   \"darkgrey\"  \"lightblue\"    \"#661100\" library(hues) swatch(cb_friendly_cols(1:16))"},{"path":"http://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"set-projects","dir":"Articles","previous_headings":"","what":"Set projects","title":"bcbioR quick start","text":"HCBC uses structured based directory organize projects. can set using: support multiple analyses type: RNAseq scRNAseq TEAseq COSMX get example code can use similar command: Use scrnaseq, teaseq cosmx get templates.","code":"tmp_dir=withr::local_tempdir() bcbio_templates(type=\"base\", outpath=tmp_dir) fs::dir_ls(tmp_dir, recurse=TRUE) #> /tmp/RtmpI7h5tU/file233c25d2e7a8/README.md #> /tmp/RtmpI7h5tU/file233c25d2e7a8/code #> /tmp/RtmpI7h5tU/file233c25d2e7a8/code/placeholder.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/data #> /tmp/RtmpI7h5tU/file233c25d2e7a8/data/readme #> /tmp/RtmpI7h5tU/file233c25d2e7a8/information.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/meta #> /tmp/RtmpI7h5tU/file233c25d2e7a8/meta/placeholder.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/scripts #> /tmp/RtmpI7h5tU/file233c25d2e7a8/scripts/placeholder #> /tmp/RtmpI7h5tU/file233c25d2e7a8/skeleton.Rmd analysis_tmp=fs::path_join(c(tmp_dir, \"reports\")) bcbio_templates(type=\"rnaseq\", outpath=analysis_tmp) fs::dir_ls(analysis_tmp, recurse=TRUE) #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/DEG.Rmd #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/PCA_variance_analysis.Rmd #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/load_data.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/params_de-example.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/params_de.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/DE/run_markdown.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/QC.Rmd #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/QC_nf-core.Rmd #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/params_qc.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/params_qc_nf-core-example.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/params_qc_nf-core.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/placeholder #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/QC/run_markdown.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/README.md #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/information.R #> /tmp/RtmpI7h5tU/file233c25d2e7a8/reports/skeleton.Rmd"},{"path":"http://bcb.io/bcbioR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Pantano Lorena. Author, maintainer.","code":""},{"path":"http://bcb.io/bcbioR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Lorena P (2024). bcbioR: Templates functions guide downstream analysis data interpretation. R package version 0.1.2, http://bcb.io/bcbioR/.","code":"@Manual{,   title = {bcbioR: Templates and functions to guide downstream analysis and data interpretation},   author = {Pantano Lorena},   year = {2024},   note = {R package version 0.1.2},   url = {http://bcb.io/bcbioR/}, }"},{"path":"http://bcb.io/bcbioR/index.html","id":"bcbior","dir":"","previous_headings":"","what":"Templates and functions to guide downstream analysis and data interpretation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"goal bcbioR create guidelines NGS data interpretation based experience Harvard Chan Bioinformatics Core everybody contributes package.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"can install development version bcbioR GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"bcbio/bcbioR\") devtools::install_github(\"bcbio/bcbioR\",ref = \"devel\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"quick-start","dir":"","previous_headings":"","what":"Quick start","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Use code generate standard project name folders. code create folders files.","code":"library(bcbioR) ## basic example code # will help you to build a folder name following HCBC naming rules bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-base-project","dir":"","previous_headings":"Quick start","what":"Set base project","title":"Templates and functions to guide downstream analysis and data interpretation","text":"use setwd() set current directory place want work. bcbioR functions automatically write whatever directory set. following code pop Rmd template populate folder HCBC data structure guidelines","code":"setwd(\"/path/to/analysis/folder\") bcbio_templates(type=\"base\", outpath=\"/path/to/analysis/folder\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-rnaseq-report-folder","dir":"","previous_headings":"Quick start","what":"Set RNAseq report folder","title":"Templates and functions to guide downstream analysis and data interpretation","text":"code populate folder HCBC data structure guidelines Rmd code: need create reports folder prior running code. create populate reports folder.","code":"bcbio_templates(type=\"rnaseq\", outpath=\"/path/to/analysis/folder/reports\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"discover-more","dir":"","previous_headings":"Quick start","what":"Discover more…","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Go vignette know vignette(\"bcbioR_quick_start\",package=\"bcbioR\")","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/index.html","id":"open-an-issue","dir":"","previous_headings":"How to Contribute","what":"Open an issue","title":"Templates and functions to guide downstream analysis and data interpretation","text":"find bug want new feature want add code templates","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"modify-the-code","dir":"","previous_headings":"How to Contribute","what":"Modify the code","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Clone repository Make sure devel branch Create new branch git checkout -b feature1 Modify code, add commit Push GitHub new branch Create PR branch devel Assignt PR Alex best practices developing: install devtools Use usethis::use_import_from(\"stringr\",\"str_replace_all\") add new function using code.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"contributors","dir":"","previous_headings":"How to Contribute","what":"Contributors","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Lorena Pantano Alex Bartlett Emma Berdan Heather Wick James Billingsley Zhu Zhuo Elizabeth Partan","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Collaborative code repository Harvard Chan Bioinformatics Core.","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Maintainer: Pantano Lorena lorena.pantano@gmail.com","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to check samplesheet for nf-core — bcbio_nfcore_check","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"Function check samplesheet nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(file)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"file path CSV file nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(system.file(\"extdata\", \"rnaseq_good.csv\", package = \"bcbioR\") ) #> Rows: 6 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (8): sample, fastq_1, fastq_2, strandedness, tissue, sex, 4_weeks, bone_... #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> All good."},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help with project name used for parent folder — bcbio_set_project","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"function ask user input : numeric code PI full name technology tissue organism project description","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"","code":"bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"string list hbc_code, project folder name","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"removes special character _. output guideline folder used can .","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help deploy analysis folder inside a project folder — bcbio_templates","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"function contains Rmd, R, md, files help structure analysis following HCBC best-practices. rnaseq, deploy: QC DE Rmd additional files help facilitate analysis needed.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"bcbio_templates(type = \"rnaseq\", outpath)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"type string indicating type analysis, supported: base rnaseq, scrnaseq, teaseq cosmx outpath string path indicating copy files ","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"Normally helper files inside report folder inside project folder.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"if (FALSE) {  bcbio_templates(\"rnaseq\", \"path_to_projects/project1/reports\")  }"},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":null,"dir":"Reference","previous_headings":"","what":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"example output varianceStabilizingTransformation show different visualization code","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"","code":"bcbio_vsd_data"},{"path":[]},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":"bcbio-vsd-data","dir":"Reference","previous_headings":"","what":"bcbio_vsd_data","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"VSD object DESeq2 data","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":null,"dir":"Reference","previous_headings":"","what":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"list colorblind-friendly colors, developed James client","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"","code":"cb_friendly_colors"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_colors.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"list of colorblind-friendly colors, developed by James and client — cb_friendly_colors","text":"object class character length 17.","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"fetch color from list by name — cb_friendly_cols","title":"fetch color from list by name — cb_friendly_cols","text":"fetch color list name","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"fetch color from list by name — cb_friendly_cols","text":"","code":"cb_friendly_cols(...)"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"fetch color from list by name — cb_friendly_cols","text":"... list color names","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":null,"dir":"Reference","previous_headings":"","what":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"access cb friendly palette name, reversing necessary","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"","code":"cb_friendly_pal(palette = \"main\", reverse = F, ...)"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_pal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"access cb friendly palette by name, reversing if necessary — cb_friendly_pal","text":"palette name palette returned reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":null,"dir":"Reference","previous_headings":"","what":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"define main colorblind-friendly palette well sub-palettes","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"","code":"cb_friendly_palettes"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"object class list length 5.","code":""},{"path":"http://bcb.io/bcbioR/reference/list_cb_friendly_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"list cb friendly colors — list_cb_friendly_cols","title":"list cb friendly colors — list_cb_friendly_cols","text":"list cb friendly colors","code":""},{"path":"http://bcb.io/bcbioR/reference/list_cb_friendly_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list cb friendly colors — list_cb_friendly_cols","text":"","code":"list_cb_friendly_cols()"},{"path":"http://bcb.io/bcbioR/reference/scale_color_cb_friendly.html","id":null,"dir":"Reference","previous_headings":"","what":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","title":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","text":"use cb friendly colors color aesthetic ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_color_cb_friendly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","text":"","code":"scale_color_cb_friendly(   palette = \"main\",   discrete = TRUE,   reverse = FALSE,   ... )"},{"path":"http://bcb.io/bcbioR/reference/scale_color_cb_friendly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"use cb friendly colors as color aesthetic with ggplot — scale_color_cb_friendly","text":"palette name palette returned discrete boolean, whether make palette discretely divided colors continuous reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":null,"dir":"Reference","previous_headings":"","what":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"use cb friendly colors fill aesthetic ggplot","code":""},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"","code":"scale_fill_cb_friendly(palette = \"main\", discrete = TRUE, reverse = FALSE, ...)"},{"path":"http://bcb.io/bcbioR/reference/scale_fill_cb_friendly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"use cb friendly colors as fill aesthetic with ggplot — scale_fill_cb_friendly","text":"palette name palette returned discrete boolean, whether make palette discretely divided colors continuous reverse boolean, reverse order colors palette ... pass ggplot","code":""},{"path":"http://bcb.io/bcbioR/news/index.html","id":"bcbior-012","dir":"Changelog","previous_headings":"","what":"bcbioR 0.1.2","title":"bcbioR 0.1.2","text":"Add draft templates TEAseq, COSMX Adapt templates nf-core rnaseq Fix sample start number Fix rRNA rate missing Add sample plots QC Add function check nfcore samplesheet Add PCA variance analysis Minor details fixed QC RNAseq report Correct metric rRNA tRNA","code":""},{"path":"http://bcb.io/bcbioR/news/index.html","id":"bcbior-011","dir":"Changelog","previous_headings":"","what":"bcbioR 0.1.1","title":"bcbioR 0.1.1","text":"Add page github Make CHECK pass Add vignette","code":""}]
+[{"path":"http://bcb.io/bcbioR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 bcbioR authors 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://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"color-blind-friendly-palette","dir":"Articles","previous_headings":"","what":"Color blind friendly palette","title":"bcbioR quick start","text":"Compatible ggplot.  get colors directly: full palette:","code":"set.seed(596) dsamp <- diamonds[sample(nrow(diamonds), 1000), ] ggplot(dsamp, aes(carat, price)) +   geom_point(aes(colour = clarity)) +   scale_color_cb_friendly() cb_friendly_cols(1:16) #>         blue light_orange  olive_green       purple         pink     sky_blue  #>    \"#2759F6\"    \"#FFD37D\" \"olivedrab3\"    \"#9176C8\"    \"#E93380\"    \"#4FAEEB\"  #>    blue_grey forest_green       yellow  dark_purple  dark_orange   army_green  #>    \"#92A6BC\"    \"#3C877B\"     \"yellow\"    \"#402999\"    \"#D5392C\"    \"#C3C380\"  #>        black    dark_grey   light_blue        brown  #>      \"black\"   \"darkgrey\"  \"lightblue\"    \"#661100\" library(hues) swatch(cb_friendly_cols(1:16))"},{"path":"http://bcb.io/bcbioR/articles/bcbioR_quick_start.html","id":"set-projects","dir":"Articles","previous_headings":"","what":"Set projects","title":"bcbioR quick start","text":"HCBC uses structured based directory organize projects. can set using: support multiple analyses type: RNAseq scRNAseq TEAseq COSMX get example code can use similar command: Use scrnaseq, teaseq cosmx get templates.","code":"tmp_dir=withr::local_tempdir() bcbio_templates(type=\"base\", outpath=tmp_dir) fs::dir_ls(tmp_dir, recurse=TRUE) #> /tmp/RtmphGxu3P/file22a383ac3fe/README.md #> /tmp/RtmphGxu3P/file22a383ac3fe/code #> /tmp/RtmphGxu3P/file22a383ac3fe/code/placeholder.R #> /tmp/RtmphGxu3P/file22a383ac3fe/data #> /tmp/RtmphGxu3P/file22a383ac3fe/data/readme #> /tmp/RtmphGxu3P/file22a383ac3fe/information.R #> /tmp/RtmphGxu3P/file22a383ac3fe/meta #> /tmp/RtmphGxu3P/file22a383ac3fe/meta/placeholder.R #> /tmp/RtmphGxu3P/file22a383ac3fe/scripts #> /tmp/RtmphGxu3P/file22a383ac3fe/scripts/placeholder #> /tmp/RtmphGxu3P/file22a383ac3fe/skeleton.Rmd analysis_tmp=fs::path_join(c(tmp_dir, \"reports\")) bcbio_templates(type=\"rnaseq\", outpath=analysis_tmp) fs::dir_ls(analysis_tmp, recurse=TRUE) #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/DE #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/DEG.Rmd #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/PCA_variance_analysis.Rmd #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/load_data.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/params_de-example.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/params_de.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/DE/run_markdown.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/QC.Rmd #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/QC_nf-core.Rmd #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/params_qc.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/params_qc_nf-core-example.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/params_qc_nf-core.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/placeholder #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/QC/run_markdown.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/README.md #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/information.R #> /tmp/RtmphGxu3P/file22a383ac3fe/reports/skeleton.Rmd"},{"path":"http://bcb.io/bcbioR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Pantano Lorena. Author, maintainer.","code":""},{"path":"http://bcb.io/bcbioR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Lorena P (2024). bcbioR: Templates functions guide downstream analysis data interpretation. R package version 0.1.3, http://bcb.io/bcbioR/.","code":"@Manual{,   title = {bcbioR: Templates and functions to guide downstream analysis and data interpretation},   author = {Pantano Lorena},   year = {2024},   note = {R package version 0.1.3},   url = {http://bcb.io/bcbioR/}, }"},{"path":"http://bcb.io/bcbioR/index.html","id":"bcbior","dir":"","previous_headings":"","what":"Templates and functions to guide downstream analysis and data interpretation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"goal bcbioR create guidelines NGS data interpretation based experience Harvard Chan Bioinformatics Core everybody contributes package.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Templates and functions to guide downstream analysis and data interpretation","text":"can install development version bcbioR GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"bcbio/bcbioR\") devtools::install_github(\"bcbio/bcbioR\",ref = \"devel\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"quick-start","dir":"","previous_headings":"","what":"Quick start","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Use code generate standard project name folders. code create folders files.","code":"library(bcbioR) ## basic example code # will help you to build a folder name following HCBC naming rules bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-base-project","dir":"","previous_headings":"Quick start","what":"Set base project","title":"Templates and functions to guide downstream analysis and data interpretation","text":"use setwd() set current directory place want work. bcbioR functions automatically write whatever directory set. following code pop Rmd template populate folder HCBC data structure guidelines","code":"setwd(\"/path/to/analysis/folder\") bcbio_templates(type=\"base\", outpath=\"/path/to/analysis/folder\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"set-rnaseq-report-folder","dir":"","previous_headings":"Quick start","what":"Set RNAseq report folder","title":"Templates and functions to guide downstream analysis and data interpretation","text":"code populate folder HCBC data structure guidelines Rmd code: need create reports folder prior running code. create populate reports folder.","code":"bcbio_templates(type=\"rnaseq\", outpath=\"/path/to/analysis/folder/reports\")"},{"path":"http://bcb.io/bcbioR/index.html","id":"discover-more","dir":"","previous_headings":"Quick start","what":"Discover more…","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Go vignette know vignette(\"bcbioR_quick_start\",package=\"bcbioR\")","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/index.html","id":"open-an-issue","dir":"","previous_headings":"How to Contribute","what":"Open an issue","title":"Templates and functions to guide downstream analysis and data interpretation","text":"find bug want new feature want add code templates","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"modify-the-code","dir":"","previous_headings":"How to Contribute","what":"Modify the code","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Clone repository Make sure devel branch Create new branch git checkout -b feature1 Modify code, add commit Push GitHub new branch Create PR branch devel Assignt PR Alex best practices developing: install devtools Use usethis::use_import_from(\"stringr\",\"str_replace_all\") add new function using code.","code":""},{"path":"http://bcb.io/bcbioR/index.html","id":"contributors","dir":"","previous_headings":"How to Contribute","what":"Contributors","title":"Templates and functions to guide downstream analysis and data interpretation","text":"Lorena Pantano Alex Bartlett Emma Berdan Heather Wick James Billingsley Zhu Zhuo Elizabeth Partan","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Collaborative code repository Harvard Chan Bioinformatics Core.","code":""},{"path":[]},{"path":"http://bcb.io/bcbioR/reference/bcbioR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"bcbioR: Templates and functions to guide downstream analysis and data interpretation — bcbioR-package","text":"Maintainer: Pantano Lorena lorena.pantano@gmail.com","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to check samplesheet for nf-core — bcbio_nfcore_check","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"Function check samplesheet nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(file)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"file path CSV file nf-core","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_nfcore_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to check samplesheet for nf-core — bcbio_nfcore_check","text":"","code":"bcbio_nfcore_check(system.file(\"extdata\", \"rnaseq_good.csv\", package = \"bcbioR\") ) #> Rows: 6 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> chr (8): sample, fastq_1, fastq_2, strandedness, tissue, sex, 4_weeks, bone_... #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> All good."},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help with project name used for parent folder — bcbio_set_project","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"function ask user input : numeric code PI full name technology tissue organism project description","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"","code":"bcbio_set_project()"},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"string list hbc_code, project folder name","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_set_project.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help with project name used for parent folder — bcbio_set_project","text":"removes special character _. output guideline folder used can .","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to help deploy analysis folder inside a project folder — bcbio_templates","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"function contains Rmd, R, md, files help structure analysis following HCBC best-practices. rnaseq, deploy: QC DE Rmd additional files help facilitate analysis needed.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"bcbio_templates(type = \"rnaseq\", outpath)"},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"type string indicating type analysis, supported: base rnaseq, scrnaseq, teaseq cosmx outpath string path indicating copy files ","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"Normally helper files inside report folder inside project folder.","code":""},{"path":"http://bcb.io/bcbioR/reference/bcbio_templates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to help deploy analysis folder inside a project folder — bcbio_templates","text":"","code":"if (FALSE) {  bcbio_templates(\"rnaseq\", \"path_to_projects/project1/reports\")  }"},{"path":"http://bcb.io/bcbioR/reference/bcbio_vsd_data.html","id":null,"dir":"Reference","previous_headings":"","what":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","title":"varianceStabilizingTransformation Object from Test Data — bcbio_vsd_data","text":"example output varianceStabilizingTransformation show different visualization 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colorblind-friendly palette well sub-palettes","code":""},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"","code":"cb_friendly_palettes"},{"path":"http://bcb.io/bcbioR/reference/cb_friendly_palettes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"define main colorblind-friendly palette as well as sub-palettes — cb_friendly_palettes","text":"object class list length 5.","code":""},{"path":"http://bcb.io/bcbioR/reference/list_cb_friendly_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"list cb friendly colors — list_cb_friendly_cols","title":"list cb friendly colors — list_cb_friendly_cols","text":"list cb friendly 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