diff --git a/404.html b/404.html
index 425045e..5d49a77 100644
--- a/404.html
+++ b/404.html
@@ -61,7 +61,7 @@ <h1>Page not found (404)</h1>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 84b527a..8e7143d 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -42,7 +42,7 @@ <h1>License</h1>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/LICENSE.html b/LICENSE.html
index 603e196..ebe04a1 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -46,7 +46,7 @@ <h1>MIT License</h1>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/articles/how-to-read-single-end-reads-from-bam-file.html b/articles/how-to-read-single-end-reads-from-bam-file.html
index 98b66c6..1883011 100644
--- a/articles/how-to-read-single-end-reads-from-bam-file.html
+++ b/articles/how-to-read-single-end-reads-from-bam-file.html
@@ -55,7 +55,7 @@
       <h1>How to read single-end reads from a BAM file</h1>
 
       <p class="author">Bioconductor Core Team</p>
-      <p class="date">2025-01-14</p>
+      <p class="date">2025-01-16</p>
 
 
       <div class="d-none name"><code></code></div>
@@ -329,7 +329,7 @@ <h1>How to read single-end reads from a BAM file</h1>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/articles/index.html b/articles/index.html
index 12e42d7..c762fca 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -44,7 +44,7 @@ <h3>All vignettes</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/authors.html b/authors.html
index 6ebaa12..3aa6f35 100644
--- a/authors.html
+++ b/authors.html
@@ -41,7 +41,31 @@ <h2>Authors</h2>
           </p>
         </li>
         <li>
-          <p><strong>Bioconductor Core Team</strong>. Author.
+          <p><strong>Hervé Pagès</strong>. Author.
+          </p>
+        </li>
+        <li>
+          <p><strong>Dan Tenenbaum</strong>. Author.
+          </p>
+        </li>
+        <li>
+          <p><strong>Valerie Obenchain</strong>. Author.
+          </p>
+        </li>
+        <li>
+          <p><strong>Marc Carlson</strong>. Author.
+          </p>
+        </li>
+        <li>
+          <p><strong>Martin Morgan</strong>. Author.
+          </p>
+        </li>
+        <li>
+          <p><strong>James Hester</strong>. Author.
+          </p>
+        </li>
+        <li>
+          <p><strong>Vince Carey</strong>. Author.
           </p>
         </li>
       </ul></div>
@@ -50,13 +74,13 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p></p>
 
-      <p>Soneson C, Bioconductor Core Team (2025).
+      <p>Soneson C, Pagès H, Tenenbaum D, Obenchain V, Carlson M, Morgan M, Hester J, Carey V (2025).
 <em>BiocHowTo: A Collection of How To Documents For Bioconductor</em>.
 R package version 0.1.0.
 </p>
       <pre>@Manual{,
   title = {BiocHowTo: A Collection of How To Documents For Bioconductor},
-  author = {Charlotte Soneson and {Bioconductor Core Team}},
+  author = {Charlotte Soneson and Hervé Pagès and Dan Tenenbaum and Valerie Obenchain and Marc Carlson and Martin Morgan and James Hester and Vince Carey},
   year = {2025},
   note = {R package version 0.1.0},
 }</pre>
@@ -67,7 +91,7 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/index.html b/index.html
index ca51ccf..2853862 100644
--- a/index.html
+++ b/index.html
@@ -57,9 +57,22 @@
 <div class="section level2">
 <h2 id="how-to-contribute">How to contribute<a class="anchor" aria-label="anchor" href="#how-to-contribute"></a>
 </h2>
-<p>To contribute, first fork this repository and create a new branch. Then copy and rename the <code>howto_template.qmd</code> file (inside the <code>vignettes</code> directory), and edit the copy accordingly. Next, add any new package that you are using to the dependencies of the package, e.g. using</p>
+<ol style="list-style-type: decimal">
+<li>Fork this repository and create a new branch.</li>
+<li>Copy and rename the <code>howto_template.qmd</code> file (inside the <code>vignettes</code> directory), and edit the copy accordingly. Please choose the name for the new vignette in such a way that it is unique and clearly indicates the content. Note that the title of the vignette should be added both to the <code>title</code> field and the <code>%\VignetteIndexEntry</code> in the YAML section.</li>
+<li>Test the vignette locally in a fresh R session, to make sure that it is self-contained and runs without errors.</li>
+<li>Add your name to the <code>Author</code> list in the <code>DESCRIPTION</code> file.</li>
+<li>Add any new package that you are using to the list of dependencies of the package, e.g. using</li>
+</ol>
 <pre><code><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu">use_package</span><span class="op">(</span><span class="st">"new_dependency"</span><span class="op">)</span></span></code></pre>
-<p>Then, push the changes to your forked repository and open a pull request to the <code>devel</code> branch of the parent repository.</p>
+<ol start="6" style="list-style-type: decimal">
+<li>Push the changes to your forked repository and open a pull request to the <code>devel</code> branch of the parent repository.</li>
+</ol>
+</div>
+<div class="section level2">
+<h2 id="how-to-suggest-a-new-topic">How to suggest a new topic<a class="anchor" aria-label="anchor" href="#how-to-suggest-a-new-topic"></a>
+</h2>
+<p>To suggest a new topic for a HowTo, open an issue and provide some more details of your suggestion.</p>
 </div>
 </div>
   </main><aside class="col-md-3"><div class="license">
@@ -82,7 +95,13 @@ <h2 data-toc-skip>Citation</h2>
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
 <li>Charlotte Soneson <br><small class="roles"> Author, maintainer </small>  </li>
-<li>Bioconductor Core Team <br><small class="roles"> Author </small>  </li>
+<li>Hervé Pagès <br><small class="roles"> Author </small>  </li>
+<li>Dan Tenenbaum <br><small class="roles"> Author </small>  </li>
+<li>Valerie Obenchain <br><small class="roles"> Author </small>  </li>
+<li>Marc Carlson <br><small class="roles"> Author </small>  </li>
+<li>Martin Morgan <br><small class="roles"> Author </small>  </li>
+<li>James Hester <br><small class="roles"> Author </small>  </li>
+<li>Vince Carey <br><small class="roles"> Author </small>  </li>
 </ul>
 </div>
 
@@ -93,7 +112,7 @@ <h2 data-toc-skip>Developers</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/pkgdown.yml b/pkgdown.yml
index bb7be95..c900c02 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1.9000
 pkgdown_sha: 6615322cb2ce15b1effcecf894123c88fa10b9c9
 articles:
   how-to-read-single-end-reads-from-bam-file: how-to-read-single-end-reads-from-bam-file.html
-last_built: 2025-01-14T14:56Z
+last_built: 2025-01-16T09:01Z
 urls:
   reference: https://csoneson.github.io/BiocHowTo/reference
   article: https://csoneson.github.io/BiocHowTo/articles
diff --git a/reference/index.html b/reference/index.html
index 35a787c..fbc6b0d 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -38,7 +38,7 @@ <h1></h1>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Charlotte Soneson, Bioconductor Core Team.</p>
+  <p>Developed by Charlotte Soneson, Hervé Pagès, Dan Tenenbaum, Valerie Obenchain, Marc Carlson, Martin Morgan, James Hester, Vince Carey.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/search.json b/search.json
index a7fac8d..60066e8 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://csoneson.github.io/BiocHowTo/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2025 BiocHowTo 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":"https://csoneson.github.io/BiocHowTo/articles/how-to-read-single-end-reads-from-bam-file.html","id":"bioconductor-packages-used-in-this-document","dir":"Articles","previous_headings":"","what":"Bioconductor packages used in this document","title":"How to read single-end reads from a BAM file","text":"pasillaBamSubset GenomicAlignments Rsamtools","code":""},{"path":"https://csoneson.github.io/BiocHowTo/articles/how-to-read-single-end-reads-from-bam-file.html","id":"how-to-read-single-end-reads-from-a-bam-file","dir":"Articles","previous_headings":"","what":"How to read single-end reads from a BAM file","title":"How to read single-end reads from a BAM file","text":"illustration, use data pasillaBamSubset data package. Several functions available reading BAM files R: GenomicAlignments::readGAlignments() GenomicAlignments::readGAlignmentPairs() GenomicAlignments::readGAlignmentsList() Rsamtools::scanBam() scanBam low-level function returns list lists discussed . See ?scanBam Rsamtools package information. Single-end reads can read readGAlignments function GenomicAlignments package. Data subsets can specified genomic position, field names, flag criteria using Rsamtools::ScanBamParam. , example import records overlap position 1 5000 negative strand chromosome 4, flag cigar metadata columns. Another approach subsetting data use Rsamtools::filterBam. function creates new BAM file records passing user-defined criteria. See ?filterBam Rsamtools package information.","code":"suppressPackageStartupMessages({     library(pasillaBamSubset) }) # Path to a bam file with single-end reads (un1 <- untreated1_chr4()) #> [1] \"/Users/runner/work/_temp/Library/pasillaBamSubset/extdata/untreated1_chr4.bam\" suppressPackageStartupMessages({     library(GenomicAlignments) }) gal <- readGAlignments(un1) class(gal) #> [1] \"GAlignments\" #> attr(,\"package\") #> [1] \"GenomicAlignments\" gal #> GAlignments object with 204355 alignments and 0 metadata columns: #>            seqnames strand       cigar    qwidth     start       end     width #>               <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> #>        [1]     chr4      -         75M        75       892       966        75 #>        [2]     chr4      -         75M        75       919       993        75 #>        [3]     chr4      +         75M        75       924       998        75 #>        [4]     chr4      +         75M        75       936      1010        75 #>        [5]     chr4      +         75M        75       949      1023        75 #>        ...      ...    ...         ...       ...       ...       ...       ... #>   [204351]     chr4      +         75M        75   1348268   1348342        75 #>   [204352]     chr4      +         75M        75   1348268   1348342        75 #>   [204353]     chr4      +         75M        75   1348268   1348342        75 #>   [204354]     chr4      -         75M        75   1348449   1348523        75 #>   [204355]     chr4      -         75M        75   1350124   1350198        75 #>                njunc #>            <integer> #>        [1]         0 #>        [2]         0 #>        [3]         0 #>        [4]         0 #>        [5]         0 #>        ...       ... #>   [204351]         0 #>   [204352]         0 #>   [204353]         0 #>   [204354]         0 #>   [204355]         0 #>   ------- #>   seqinfo: 8 sequences from an unspecified genome suppressPackageStartupMessages({     library(Rsamtools) }) what <- c(\"flag\", \"cigar\") which <- GRanges(\"chr4\", IRanges(1, 5000)) flag <- scanBamFlag(isMinusStrand = TRUE) param <- ScanBamParam(which = which, what = what, flag = flag) neg <- readGAlignments(un1, param = param) neg #> GAlignments object with 37 alignments and 2 metadata columns: #>        seqnames strand       cigar    qwidth     start       end     width #>           <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> #>    [1]     chr4      -         75M        75       892       966        75 #>    [2]     chr4      -         75M        75       919       993        75 #>    [3]     chr4      -         75M        75       967      1041        75 #>    [4]     chr4      -         75M        75      1035      1109        75 #>    [5]     chr4      -         75M        75      1236      1310        75 #>    ...      ...    ...         ...       ...       ...       ...       ... #>   [33]     chr4      -         75M        75      4995      5069        75 #>   [34]     chr4      -         75M        75      4997      5071        75 #>   [35]     chr4      -         75M        75      4997      5071        75 #>   [36]     chr4      -         75M        75      4998      5072        75 #>   [37]     chr4      -         75M        75      4999      5073        75 #>            njunc |      flag       cigar #>        <integer> | <integer> <character> #>    [1]         0 |        16         75M #>    [2]         0 |        16         75M #>    [3]         0 |        16         75M #>    [4]         0 |        16         75M #>    [5]         0 |        16         75M #>    ...       ... .       ...         ... #>   [33]         0 |        16         75M #>   [34]         0 |        16         75M #>   [35]         0 |        16         75M #>   [36]         0 |        16         75M #>   [37]         0 |        16         75M #>   ------- #>   seqinfo: 8 sequences from an unspecified genome"},{"path":"https://csoneson.github.io/BiocHowTo/articles/how-to-read-single-end-reads-from-bam-file.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"How to read single-end reads from a BAM file","text":"","code":"sessionInfo() #> R Under development (unstable) (2025-01-03 r87521) #> Platform: aarch64-apple-darwin20 #> Running under: macOS Sonoma 14.7.2 #>  #> Matrix products: default #> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib  #> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0 #>  #> locale: #> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 #>  #> time zone: UTC #> tzcode source: internal #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] GenomicAlignments_1.43.0    Rsamtools_2.23.1            #>  [3] Biostrings_2.75.3           XVector_0.47.2              #>  [5] SummarizedExperiment_1.37.0 Biobase_2.67.0              #>  [7] MatrixGenerics_1.19.1       matrixStats_1.5.0           #>  [9] GenomicRanges_1.59.1        GenomeInfoDb_1.43.2         #> [11] IRanges_2.41.2              S4Vectors_0.45.2            #> [13] BiocGenerics_0.53.3         generics_0.1.3              #> [15] pasillaBamSubset_0.45.0     BiocStyle_2.35.0            #>  #> loaded via a namespace (and not attached): #>  [1] Matrix_1.7-1            jsonlite_1.8.9          compiler_4.5.0          #>  [4] BiocManager_1.30.25     crayon_1.5.3            bitops_1.0-9            #>  [7] parallel_4.5.0          BiocParallel_1.41.0     yaml_2.3.10             #> [10] fastmap_1.2.0           lattice_0.22-6          R6_2.5.1                #> [13] S4Arrays_1.7.1          knitr_1.49              DelayedArray_0.33.3     #> [16] GenomeInfoDbData_1.2.13 rlang_1.1.4             xfun_0.50               #> [19] SparseArray_1.7.2       cli_3.6.3               digest_0.6.37           #> [22] grid_4.5.0              evaluate_1.0.3          codetools_0.2-20        #> [25] abind_1.4-8             rmarkdown_2.29          httr_1.4.7              #> [28] tools_4.5.0             htmltools_0.5.8.1       UCSC.utils_1.3.0"},{"path":"https://csoneson.github.io/BiocHowTo/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Charlotte Soneson. Author, maintainer. Bioconductor Core Team. Author.","code":""},{"path":"https://csoneson.github.io/BiocHowTo/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Soneson C, Bioconductor Core Team (2025). BiocHowTo: Collection Documents Bioconductor. R package version 0.1.0.","code":"@Manual{,   title = {BiocHowTo: A Collection of How To Documents For Bioconductor},   author = {Charlotte Soneson and {Bioconductor Core Team}},   year = {2025},   note = {R package version 0.1.0}, }"},{"path":"https://csoneson.github.io/BiocHowTo/index.html","id":"biochowto","dir":"","previous_headings":"","what":"A Collection of How To Documents For Bioconductor","title":"A Collection of How To Documents For Bioconductor","text":"repository contains short, stand-alone “” documents related Bioconductor.","code":""},{"path":"https://csoneson.github.io/BiocHowTo/index.html","id":"how-to-contribute","dir":"","previous_headings":"","what":"How to contribute","title":"A Collection of How To Documents For Bioconductor","text":"contribute, first fork repository create new branch. copy rename howto_template.qmd file (inside vignettes directory), edit copy accordingly. Next, add new package using dependencies package, e.g. using , push changes forked repository open pull request devel branch parent repository.","code":"usethis::use_package(\"new_dependency\")"}]
+[{"path":"https://csoneson.github.io/BiocHowTo/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2025 BiocHowTo 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":"https://csoneson.github.io/BiocHowTo/articles/how-to-read-single-end-reads-from-bam-file.html","id":"bioconductor-packages-used-in-this-document","dir":"Articles","previous_headings":"","what":"Bioconductor packages used in this document","title":"How to read single-end reads from a BAM file","text":"pasillaBamSubset GenomicAlignments Rsamtools","code":""},{"path":"https://csoneson.github.io/BiocHowTo/articles/how-to-read-single-end-reads-from-bam-file.html","id":"how-to-read-single-end-reads-from-a-bam-file","dir":"Articles","previous_headings":"","what":"How to read single-end reads from a BAM file","title":"How to read single-end reads from a BAM file","text":"illustration, use data pasillaBamSubset data package. Several functions available reading BAM files R: GenomicAlignments::readGAlignments() GenomicAlignments::readGAlignmentPairs() GenomicAlignments::readGAlignmentsList() Rsamtools::scanBam() scanBam low-level function returns list lists discussed . See ?scanBam Rsamtools package information. Single-end reads can read readGAlignments function GenomicAlignments package. Data subsets can specified genomic position, field names, flag criteria using Rsamtools::ScanBamParam. , example import records overlap position 1 5000 negative strand chromosome 4, flag cigar metadata columns. Another approach subsetting data use Rsamtools::filterBam. function creates new BAM file records passing user-defined criteria. See ?filterBam Rsamtools package information.","code":"suppressPackageStartupMessages({     library(pasillaBamSubset) }) # Path to a bam file with single-end reads (un1 <- untreated1_chr4()) #> [1] \"/Users/runner/work/_temp/Library/pasillaBamSubset/extdata/untreated1_chr4.bam\" suppressPackageStartupMessages({     library(GenomicAlignments) }) gal <- readGAlignments(un1) class(gal) #> [1] \"GAlignments\" #> attr(,\"package\") #> [1] \"GenomicAlignments\" gal #> GAlignments object with 204355 alignments and 0 metadata columns: #>            seqnames strand       cigar    qwidth     start       end     width #>               <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> #>        [1]     chr4      -         75M        75       892       966        75 #>        [2]     chr4      -         75M        75       919       993        75 #>        [3]     chr4      +         75M        75       924       998        75 #>        [4]     chr4      +         75M        75       936      1010        75 #>        [5]     chr4      +         75M        75       949      1023        75 #>        ...      ...    ...         ...       ...       ...       ...       ... #>   [204351]     chr4      +         75M        75   1348268   1348342        75 #>   [204352]     chr4      +         75M        75   1348268   1348342        75 #>   [204353]     chr4      +         75M        75   1348268   1348342        75 #>   [204354]     chr4      -         75M        75   1348449   1348523        75 #>   [204355]     chr4      -         75M        75   1350124   1350198        75 #>                njunc #>            <integer> #>        [1]         0 #>        [2]         0 #>        [3]         0 #>        [4]         0 #>        [5]         0 #>        ...       ... #>   [204351]         0 #>   [204352]         0 #>   [204353]         0 #>   [204354]         0 #>   [204355]         0 #>   ------- #>   seqinfo: 8 sequences from an unspecified genome suppressPackageStartupMessages({     library(Rsamtools) }) what <- c(\"flag\", \"cigar\") which <- GRanges(\"chr4\", IRanges(1, 5000)) flag <- scanBamFlag(isMinusStrand = TRUE) param <- ScanBamParam(which = which, what = what, flag = flag) neg <- readGAlignments(un1, param = param) neg #> GAlignments object with 37 alignments and 2 metadata columns: #>        seqnames strand       cigar    qwidth     start       end     width #>           <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> #>    [1]     chr4      -         75M        75       892       966        75 #>    [2]     chr4      -         75M        75       919       993        75 #>    [3]     chr4      -         75M        75       967      1041        75 #>    [4]     chr4      -         75M        75      1035      1109        75 #>    [5]     chr4      -         75M        75      1236      1310        75 #>    ...      ...    ...         ...       ...       ...       ...       ... #>   [33]     chr4      -         75M        75      4995      5069        75 #>   [34]     chr4      -         75M        75      4997      5071        75 #>   [35]     chr4      -         75M        75      4997      5071        75 #>   [36]     chr4      -         75M        75      4998      5072        75 #>   [37]     chr4      -         75M        75      4999      5073        75 #>            njunc |      flag       cigar #>        <integer> | <integer> <character> #>    [1]         0 |        16         75M #>    [2]         0 |        16         75M #>    [3]         0 |        16         75M #>    [4]         0 |        16         75M #>    [5]         0 |        16         75M #>    ...       ... .       ...         ... #>   [33]         0 |        16         75M #>   [34]         0 |        16         75M #>   [35]         0 |        16         75M #>   [36]         0 |        16         75M #>   [37]         0 |        16         75M #>   ------- #>   seqinfo: 8 sequences from an unspecified genome"},{"path":"https://csoneson.github.io/BiocHowTo/articles/how-to-read-single-end-reads-from-bam-file.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session info","title":"How to read single-end reads from a BAM file","text":"","code":"sessionInfo() #> R Under development (unstable) (2025-01-03 r87521) #> Platform: aarch64-apple-darwin20 #> Running under: macOS Sonoma 14.7.2 #>  #> Matrix products: default #> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib  #> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0 #>  #> locale: #> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 #>  #> time zone: UTC #> tzcode source: internal #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] GenomicAlignments_1.43.0    Rsamtools_2.23.1            #>  [3] Biostrings_2.75.3           XVector_0.47.2              #>  [5] SummarizedExperiment_1.37.0 Biobase_2.67.0              #>  [7] MatrixGenerics_1.19.1       matrixStats_1.5.0           #>  [9] GenomicRanges_1.59.1        GenomeInfoDb_1.43.2         #> [11] IRanges_2.41.2              S4Vectors_0.45.2            #> [13] BiocGenerics_0.53.3         generics_0.1.3              #> [15] pasillaBamSubset_0.45.0     BiocStyle_2.35.0            #>  #> loaded via a namespace (and not attached): #>  [1] Matrix_1.7-1            jsonlite_1.8.9          compiler_4.5.0          #>  [4] BiocManager_1.30.25     crayon_1.5.3            bitops_1.0-9            #>  [7] parallel_4.5.0          BiocParallel_1.41.0     yaml_2.3.10             #> [10] fastmap_1.2.0           lattice_0.22-6          R6_2.5.1                #> [13] S4Arrays_1.7.1          knitr_1.49              DelayedArray_0.33.3     #> [16] GenomeInfoDbData_1.2.13 rlang_1.1.4             xfun_0.50               #> [19] SparseArray_1.7.2       cli_3.6.3               digest_0.6.37           #> [22] grid_4.5.0              evaluate_1.0.3          codetools_0.2-20        #> [25] abind_1.4-8             rmarkdown_2.29          httr_1.4.7              #> [28] tools_4.5.0             htmltools_0.5.8.1       UCSC.utils_1.3.0"},{"path":"https://csoneson.github.io/BiocHowTo/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Charlotte Soneson. Author, maintainer. Hervé Pagès. Author. Dan Tenenbaum. Author. Valerie Obenchain. Author. Marc Carlson. Author. Martin Morgan. Author. James Hester. Author. Vince Carey. Author.","code":""},{"path":"https://csoneson.github.io/BiocHowTo/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Soneson C, Pagès H, Tenenbaum D, Obenchain V, Carlson M, Morgan M, Hester J, Carey V (2025). BiocHowTo: Collection Documents Bioconductor. R package version 0.1.0.","code":"@Manual{,   title = {BiocHowTo: A Collection of How To Documents For Bioconductor},   author = {Charlotte Soneson and Hervé Pagès and Dan Tenenbaum and Valerie Obenchain and Marc Carlson and Martin Morgan and James Hester and Vince Carey},   year = {2025},   note = {R package version 0.1.0}, }"},{"path":"https://csoneson.github.io/BiocHowTo/index.html","id":"biochowto","dir":"","previous_headings":"","what":"A Collection of How To Documents For Bioconductor","title":"A Collection of How To Documents For Bioconductor","text":"repository contains short, stand-alone “” documents related Bioconductor.","code":""},{"path":"https://csoneson.github.io/BiocHowTo/index.html","id":"how-to-contribute","dir":"","previous_headings":"","what":"How to contribute","title":"A Collection of How To Documents For Bioconductor","text":"Fork repository create new branch. Copy rename howto_template.qmd file (inside vignettes directory), edit copy accordingly. Please choose name new vignette way unique clearly indicates content. Note title vignette added title field %\\VignetteIndexEntry YAML section. Test vignette locally fresh R session, make sure self-contained runs without errors. Add name Author list DESCRIPTION file. Add new package using list dependencies package, e.g. using Push changes forked repository open pull request devel branch parent repository.","code":"usethis::use_package(\"new_dependency\")"},{"path":"https://csoneson.github.io/BiocHowTo/index.html","id":"how-to-suggest-a-new-topic","dir":"","previous_headings":"","what":"How to suggest a new topic","title":"A Collection of How To Documents For Bioconductor","text":"suggest new topic HowTo, open issue provide details suggestion.","code":""}]