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 <meta name="author" content="Daniela Cassol">
 <meta name="author" content="Johannes Rainer">
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@@ -116,6 +118,7 @@ <h1>
 <li><a class="" href="cmavericks-best-practices.html"><span class="header-section-number">E</span> C++/Mavericks Best Practices</a></li>
 <li><a class="" href="man-links.html"><span class="header-section-number">F</span> Debug: Links in Rd files</a></li>
 <li><a class="" href="booknews.html"><span class="header-section-number">G</span> NEWS</a></li>
+<li><a class="" href="references-1.html"><span class="header-section-number">H</span> References</a></li>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-06-03.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd, Marcel Ramos Pérez, Martin Morgan. It was last built on 2025-06-06.</p>
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bioconductor-package-submissions.html

@@ -9,14 +9,16 @@
 <meta name="author" content="Daniela Cassol">
 <meta name="author" content="Johannes Rainer">
 <meta name="author" content="Lori Shepherd">
-<meta name="description" content="Introduction Types of Packages Package Naming Policy Author/Maintainer Expectations Submission Experiment data package Annotation package Workflow package Review Process Following Acceptance...">
+<meta name="author" content="Marcel Ramos Pérez">
+<meta name="author" content="Martin Morgan">
+<meta name="description" content="1.1 Introduction To submit a package to Bioconductor the package should: Address areas of high-throughput genomic analysis, e.g., sequencing, expression and other microarrays, flow cytometry, mass...">
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@@ -116,6 +118,7 @@ <h1>
 <li><a class="" href="cmavericks-best-practices.html"><span class="header-section-number">E</span> C++/Mavericks Best Practices</a></li>
 <li><a class="" href="man-links.html"><span class="header-section-number">F</span> Debug: Links in Rd files</a></li>
 <li><a class="" href="booknews.html"><span class="header-section-number">G</span> NEWS</a></li>
+<li><a class="" href="references-1.html"><span class="header-section-number">H</span> References</a></li>
 </ul>
 
         <div class="book-extra">
@@ -127,19 +130,6 @@ <h1>
 <h1>
 <span class="header-section-number">1</span> Bioconductor Package Submissions<a class="anchor" aria-label="anchor" href="#bioconductor-package-submissions"><i class="fas fa-link"></i></a>
 </h1>
-<ul>
-<li><a href="bioconductor-package-submissions.html#subintro">Introduction</a></li>
-<li><a href="bioconductor-package-submissions.html#type">Types of Packages</a></li>
-<li><a href="bioconductor-package-submissions.html#naming">Package Naming Policy</a></li>
-<li><a href="bioconductor-package-submissions.html#author">Author/Maintainer Expectations</a></li>
-<li><a href="bioconductor-package-submissions.html#submission">Submission</a></li>
-<li><a href="bioconductor-package-submissions.html#experPackage">Experiment data package</a></li>
-<li><a href="bioconductor-package-submissions.html#annPackage">Annotation package</a></li>
-<li><a href="bioconductor-package-submissions.html#workPackage">Workflow package</a></li>
-<li><a href="bioconductor-package-submissions.html#whattoexpect">Review Process</a></li>
-<li><a href="bioconductor-package-submissions.html#afteraccept">Following Acceptance</a></li>
-<li><a href="bioconductor-package-submissions.html#support">Additional Support</a></li>
-</ul>
 <div id="subintro" class="section level2" number="1.1">
 <h2>
 <span class="header-section-number">1.1</span> Introduction<a class="anchor" aria-label="anchor" href="#subintro"><i class="fas fa-link"></i></a>
@@ -161,7 +151,7 @@ <h2>
 <li>Comply with <a href="develop-overview.html#develop-overview">Package Guidelines</a>.</li>
 <li>Your package cannot depend on any package (or version of a package)
 that is not (yet) available on CRAN or <em>Bioconductor</em>. The package should work
-with whatever current version of the package is publically available.</li>
+with whatever current version of the package is publicly available.</li>
 </ul>
 </div>
 <div id="type" class="section level2" number="1.2">
@@ -174,7 +164,7 @@ <h2>
 <ul>
 <li><p>Software Packages. Most packages contributed by users are software
 packages. Software packages provide implementation of algorithms
-(e.g. statistical analysis), access to resources (e.g. biomart, or NCBI) or
+(e.g. statistical analysis), access to resources (e.g. <code>biomaRt</code>, or NCBI) or
 visualizations (e.g. volcano plots, pathways plots). Instructions for creating
 Software packages can be found here: <a href="develop-overview.html#develop-overview">Package guidelines</a>.</p></li>
 <li><p><a href="bioconductor-package-submissions.html#annPackage">Annotation packages</a> are database-like packages that provide
@@ -217,7 +207,7 @@ <h2>
 package contributor discontinues package maintenance. See Bioconductor’s package
 <a href="package-end-of-life-policy.html#package-end-of-life-policy">end-of-life policy</a> for more details.</p></li>
 <li><p>Uniqueness of package name. Packages should be named in a way that does not
-conflict (irrespective of case) with any current or past BIOCONDUCTOR package,
+conflict (irrespective of case) with any current or past Bioconductor package,
 nor any current or past CRAN package.</p></li>
 </ol>
 <p>See <a href="package-name.html#package-name">Package naming guidelines</a> for more guidelines.</p>
@@ -231,11 +221,11 @@ <h2>
 <ul>
 <li>
 <p>Follow Bioconductor guidelines</p>
-<p>These include standard <a href="develop-overview.html#develop-overview">guidelines</a>, <a href="versionnum.html#versionnum">version numbering</a>,
-<a href="r-code.html#r-code">coding style</a>, <a href="general.html#correctness-space-and-time">code performance
-requirements</a>, <a href="general.html#memory">memory usage</a>, <a href="important-bioconductor-package-development-features.html#reusebioc">using
-existing data classes</a>, and the other requirements described
-below.</p>
+<p>These include standard <a href="develop-overview.html#develop-overview">guidelines</a>,
+<a href="versionnum.html#versionnum">version numbering</a>, <a href="r-code.html#r-code">coding style</a>,
+<a href="general.html#correctness-space-and-time">code performance requirements</a>,
+<a href="general.html#memory">memory usage</a>, <a href="important-bioconductor-package-development-features.html#reusebioc">using existing data classes</a>,
+and the other requirements described below.</p>
 </li>
 <li>
 <p>Follow the release cycle of Bioconductor</p>
@@ -287,11 +277,11 @@ <h2>
 It is important to promptly respond to bug reports and questions either on
 the <a href="https://support.bioconductor.org/"><em>Bioconductor</em> support site</a> post or directly to developers.
 Some maintainers prefer to indicate a <code>BugReports:</code> field in their package’s
-DESCRIPTION file. This field indicates a particular web page for submitting
+<code>DESCRIPTION</code> file. This field indicates a particular web page for submitting
 bug reports and questions.</p>
 </li>
-<li><p>Ensure the maintainer email in the DESCRIPTION stays accurate and
-reachable. The maintainer email in the DESCRIPTION is the definitive contact
+<li><p>Ensure the maintainer email in the <code>DESCRIPTION</code> stays accurate and
+reachable. The maintainer email in the <code>DESCRIPTION</code> is the definitive contact
 <em>Bioconductor</em> will use. It is important to keep this email up-to-date to
 ensure we can contact you if your package is failing or to notify you of any
 important upcoming impactful events. If the email is not reachable your
@@ -312,7 +302,7 @@ <h2>
 the issue you are opening. You cannot specify any alternative branches; the
 default branch is utilized. The default branch must contain only package
 code. Any files or directories for other applications (Github Actions,
-devtool, etc) should be in a different branch. If you are submitting two
+devtools, etc) should be in a different branch. If you are submitting two
 highly related packages or circular dependent packages please see
 <a href="https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages">here</a>. The lighter dependent or package that can be installed without
 a dependency should be submitted first; this is generally the associated data
@@ -484,7 +474,7 @@ <h2>
 <a href="versionnum.html#versionnum">Version numbering</a> guidelines. If developers don’t
 bump the version, the changes made to their package <em>do not propagate</em>
 to the <em>Bioconductor</em> web site and package repository.</li>
-<li>Devlopers should make sure the maintainer email in the DESCRIPTION stays
+<li>Developers should make sure the maintainer email in the <code>DESCRIPTION</code> stays
 accurate and reachable.</li>
 </ul>
 </div>
@@ -548,7 +538,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-06-03.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd, Marcel Ramos Pérez, Martin Morgan. It was last built on 2025-06-06.</p>
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booknews.html

@@ -9,6 +9,8 @@
 <meta name="author" content="Daniela Cassol">
 <meta name="author" content="Johannes Rainer">
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+<meta name="author" content="Marcel Ramos Pérez">
+<meta name="author" content="Martin Morgan">
 <meta name="description" content="G.1 Version 1.0.1 (2021-08-19) Add a dedicated section on the package name.  G.2 Version 1.0.0 (2021-06-02) Initial definition of the package development guidelines based on Bioconductor package...">
 <meta name="generator" content="bookdown 0.43 with bs4_book()">
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@@ -116,6 +118,7 @@ <h1>
 <li><a class="" href="cmavericks-best-practices.html"><span class="header-section-number">E</span> C++/Mavericks Best Practices</a></li>
 <li><a class="" href="man-links.html"><span class="header-section-number">F</span> Debug: Links in Rd files</a></li>
 <li><a class="active" href="booknews.html"><span class="header-section-number">G</span> NEWS</a></li>
+<li><a class="" href="references-1.html"><span class="header-section-number">H</span> References</a></li>
 </ul>
 
         <div class="book-extra">
@@ -143,23 +146,11 @@ <h2>
 <li>Initial definition of the package development guidelines based on
 Bioconductor package guidelines listed on main Bioconductor.org website.</li>
 </ul>
-<div id="refs" class="references csl-bib-body hanging-indent" entry-spacing="0">
-<div id="ref-Soneson2025-zr" class="csl-entry">
-Soneson, Charlotte, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer, Hervé Pagès, and Vincent J Carey. 2025. <span>“Eleven Quick Tips for Writing a Bioconductor Package.”</span> <em>PLoS Comput. Biol.</em> 21 (3): e1012856. <a href="https://doi.org/10.1371/journal.pcbi.1012856">https://doi.org/10.1371/journal.pcbi.1012856</a>.
 </div>
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 <div class="prev"><a href="man-links.html"><span class="header-section-number">F</span> Debug: Links in Rd files</a></div>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-06-03.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd, Marcel Ramos Pérez, Martin Morgan. It was last built on 2025-06-06.</p>
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branch-rename-faqs.html

@@ -9,6 +9,8 @@
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 <li><a class="" href="booknews.html"><span class="header-section-number">G</span> NEWS</a></li>
+<li><a class="" href="references-1.html"><span class="header-section-number">H</span> References</a></li>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-06-03.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd, Marcel Ramos Pérez, Martin Morgan. It was last built on 2025-06-06.</p>
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c-fortran.html

@@ -9,6 +9,8 @@
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 <meta name="author" content="Johannes Rainer">
 <meta name="author" content="Lori Shepherd">
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 <li><a class="" href="booknews.html"><span class="header-section-number">G</span> NEWS</a></li>
+<li><a class="" href="references-1.html"><span class="header-section-number">H</span> References</a></li>
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@@ -207,7 +210,7 @@ <h3>
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-    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd. It was last built on 2025-06-03.</p>
+    <p>"<strong>Bioconductor Packages: Development, Maintenance, and Peer Review</strong>" was written by Kevin Rue-Albrecht, Daniela Cassol, Johannes Rainer, Lori Shepherd, Marcel Ramos Pérez, Martin Morgan. It was last built on 2025-06-06.</p>
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