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5c3915c
update L1.1
billila May 18, 2026
b2d2af2
update L1.2
billila May 18, 2026
2b05a48
update L1.4
billila May 18, 2026
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update L1.5
billila May 18, 2026
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update L1_intro
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update L1.3
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check regression lab
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4 changes: 2 additions & 2 deletions intro-to-r-bioc/L1.1-r-intro.Rmd
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Expand Up @@ -21,11 +21,11 @@ knitr::opts_chunk$set(

**Original Authors:** Martin Morgan, Sonali Arora, Lori Shepherd<br />
**Presenting Author:** [Davide Risso][], [Ilaria Billato][]</br >
**Date:** 6-11 July, 2025</br >
**Date:** 24-29 May, 2026</br >
**Back:** [Monday labs](lab-1-intro-to-r-bioc.html)

[Davide Risso]: mailto: davide.risso@unipd.it
[Ilaria Billato]: mailto: ilaria.billato@phd.unipd.it
[Ilaria Billato]: mailto: ilaria.billato@unipd.it


**Objective**: Gain confidence working with base R commands and data
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4 changes: 2 additions & 2 deletions intro-to-r-bioc/L1.2-tidy-r-intro.Rmd
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**Original Authors:** Martin Morgan, Sonali Arora, Lori Shepherd<br />
**Presenting Author:** [Davide Risso][], [Ilaria Billato][]</br >
**Date:** 6-11 July, 2025</br >
**Date:** 24-29 May, 2026</br >
**Back:** [Monday labs](lab-1-intro-to-r-bioc.html)

[Davide Risso]: mailto: davide.risso@unipd.it
[Ilaria Billato]: mailto: ilaria.billato@phd.unipd.it
[Ilaria Billato]: mailto: ilaria.billato@unipd.it


**Objective**: Gain confidence working with 'tidy' R commands and data
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4 changes: 2 additions & 2 deletions intro-to-r-bioc/L1.3-starting-an-analysis.Rmd
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Expand Up @@ -25,11 +25,11 @@ suppressPackageStartupMessages({

**Original Authors:** Martin Morgan, Sonali Arora, Lori Shepherd<br />
**Presenting Author:** [Davide Risso][], [Ilaria Billato][]</br >
**Date:** 6-11 July, 2025</br >
**Date:** 24-29 May, 2026</br >
**Back:** [Monday labs](lab-1-intro-to-r-bioc.html)

[Davide Risso]: mailto: davide.risso@unipd.it
[Ilaria Billato]: mailto: ilaria.billato@phd.unipd.it
[Ilaria Billato]: mailto: ilaria.billato@unipd.it

**Objective**: An overview of software available in _Bioconductor_.

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55 changes: 27 additions & 28 deletions intro-to-r-bioc/L1.3-starting-an-analysis.html
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<meta name="date" content="2025-07-04" />
<meta name="date" content="2026-05-18" />

<title>Lab 1.3: Starting an analysis</title>

Expand Down Expand Up @@ -701,7 +701,7 @@


<h1 class="title toc-ignore">Lab 1.3: Starting an analysis</h1>
<h4 class="date">4 July 2025</h4>
<h4 class="date">18 May 2026</h4>

</div>

Expand Down Expand Up @@ -742,8 +742,8 @@ <h1>Contents</h1>
});
</script>
<p><strong>Original Authors:</strong> Martin Morgan, Sonali Arora, Lori Shepherd<br />
<strong>Presenting Author:</strong> <a href="mailto:%20davide.risso@unipd.it">Davide Risso</a>, <a href="mailto:%20ilaria.billato@phd.unipd.it">Ilaria Billato</a></br>
<strong>Date:</strong> 6-11 July, 2025</br>
<strong>Presenting Author:</strong> <a href="mailto:%20davide.risso@unipd.it">Davide Risso</a>, <a href="mailto:%20ilaria.billato@unipd.it">Ilaria Billato</a></br>
<strong>Date:</strong> 24-29 May, 2026</br>
<strong>Back:</strong> <a href="lab-1-intro-to-r-bioc.html">Monday labs</a></p>
<p><strong>Objective</strong>: An overview of software available in <em>Bioconductor</em>.</p>
<p><strong>Lessons learned</strong>:</p>
Expand Down Expand Up @@ -777,7 +777,7 @@ <h2><span class="header-section-number">1.1</span> Packages, vignettes, work flo
<ul>
<li>1750 software packages</li>
<li>Discover and navigate via <a href="http://bioconductor.org/packages/release/BiocViews.html#___Software">biocViews</a></li>
<li>Package ‘landing page’, e.g., <em><a href="https://bioconductor.org/packages/3.21/Gviz">Gviz</a></em>
<li>Package ‘landing page’, e.g., <em><a href="https://bioconductor.org/packages/3.23/Gviz">Gviz</a></em>
<ul>
<li>Title, author / maintainer, short description, citation,
installation instructions, …, download statistics</li>
Expand Down Expand Up @@ -1135,9 +1135,9 @@ <h1><span class="header-section-number">5</span> End matter</h1>
<div id="session-info" class="section level2" number="5.1">
<h2><span class="header-section-number">5.1</span> Session Info</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>## R version 4.5.1 (2025-06-13)
<pre><code>## R version 4.6.0 (2026-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## Running under: Ubuntu 24.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
Expand All @@ -1159,29 +1159,28 @@ <h2><span class="header-section-number">5.1</span> Session Info</h2>
## [8] base
##
## other attached packages:
## [1] GenomicAlignments_1.44.0 Rsamtools_2.24.0
## [3] SummarizedExperiment_1.38.1 Biobase_2.68.0
## [5] MatrixGenerics_1.20.0 matrixStats_1.5.0
## [7] GenomicRanges_1.60.0 Biostrings_2.76.0
## [9] GenomeInfoDb_1.44.0 XVector_0.48.0
## [11] IRanges_2.42.0 S4Vectors_0.46.0
## [13] BiocGenerics_0.54.0 generics_0.1.4
## [15] BiocStyle_2.36.0
## [1] GenomicAlignments_1.48.0 Rsamtools_2.28.0
## [3] SummarizedExperiment_1.42.0 Biobase_2.72.0
## [5] MatrixGenerics_1.24.0 matrixStats_1.5.0
## [7] GenomicRanges_1.64.0 Biostrings_2.80.0
## [9] Seqinfo_1.2.0 XVector_0.52.0
## [11] IRanges_2.46.0 S4Vectors_0.50.1
## [13] BiocGenerics_0.58.1 generics_0.1.4
## [15] BiocStyle_2.40.0
##
## loaded via a namespace (and not attached):
## [1] Matrix_1.7-3 jsonlite_2.0.0 compiler_4.5.1
## [4] BiocManager_1.30.26 crayon_1.5.3 bitops_1.0-9
## [7] parallel_4.5.1 jquerylib_0.1.4 BiocParallel_1.42.1
## [10] yaml_2.3.10 fastmap_1.2.0 lattice_0.22-7
## [13] R6_2.6.1 S4Arrays_1.8.1 knitr_1.50
## [16] DelayedArray_0.34.1 bookdown_0.43 GenomeInfoDbData_1.2.14
## [19] bslib_0.9.0 rlang_1.1.6 cachem_1.1.0
## [22] xfun_0.52 sass_0.4.10 SparseArray_1.8.0
## [25] cli_3.6.5 digest_0.6.37 grid_4.5.1
## [28] rstudioapi_0.17.1 lifecycle_1.0.4 evaluate_1.0.4
## [31] codetools_0.2-20 abind_1.4-8 rmarkdown_2.29
## [34] httr_1.4.7 tools_4.5.1 htmltools_0.5.8.1
## [37] UCSC.utils_1.4.0</code></pre>
## [1] Matrix_1.7-5 jsonlite_2.0.0 compiler_4.6.0
## [4] BiocManager_1.30.27 crayon_1.5.3 bitops_1.0-9
## [7] parallel_4.6.0 jquerylib_0.1.4 BiocParallel_1.46.0
## [10] yaml_2.3.12 fastmap_1.2.0 lattice_0.22-9
## [13] R6_2.6.1 S4Arrays_1.12.0 knitr_1.51
## [16] DelayedArray_0.38.1 bookdown_0.46 bslib_0.11.0
## [19] rlang_1.2.0 cachem_1.1.0 xfun_0.57
## [22] sass_0.4.10 otel_0.2.0 SparseArray_1.12.2
## [25] cli_3.6.6 digest_0.6.39 grid_4.6.0
## [28] rstudioapi_0.18.0 lifecycle_1.0.5 evaluate_1.0.5
## [31] cigarillo_1.2.0 codetools_0.2-20 abind_1.4-8
## [34] rmarkdown_2.31 tools_4.6.0 htmltools_0.5.9</code></pre>
</div>
<div id="acknowledgements" class="section level2" number="5.2">
<h2><span class="header-section-number">5.2</span> Acknowledgements</h2>
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130 changes: 66 additions & 64 deletions intro-to-r-bioc/L1.4-bioc-data-representation.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.9.4">
<meta name="generator" content="quarto-1.8.25">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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<script src="L1.4-bioc-data-representation_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="L1.4-bioc-data-representation_files/libs/quarto-html/anchor.min.js"></script>
<link href="L1.4-bioc-data-representation_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="L1.4-bioc-data-representation_files/libs/quarto-html/quarto-syntax-highlighting-485605091aded536db53fb751867c3cd.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<link href="L1.4-bioc-data-representation_files/libs/quarto-html/quarto-syntax-highlighting-7b89279ff1a6dce999919e0e67d4d9ec.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="L1.4-bioc-data-representation_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="L1.4-bioc-data-representation_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="L1.4-bioc-data-representation_files/libs/bootstrap/bootstrap-21bde2f931a99665fbf83a991a54851e.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
<link href="L1.4-bioc-data-representation_files/libs/bootstrap/bootstrap-0f84be458ac1676c4ed837d23416e910.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
<script src="L1.4-bioc-data-representation_files/libs/quarto-contrib/glightbox/glightbox.min.js"></script>
<link href="L1.4-bioc-data-representation_files/libs/quarto-contrib/glightbox/glightbox.min.css" rel="stylesheet">
<link href="L1.4-bioc-data-representation_files/libs/quarto-contrib/glightbox/lightbox.css" rel="stylesheet">
Expand Down Expand Up @@ -175,7 +175,7 @@ <h1 class="title">Lab 1.4: Representations for biomolecular sequences</h1>
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>Martin Morgan, Sonali Arora, Lori Shepherd, <a href="mailto:davide.risso@unipd.it">Davide Risso</a>, <a href="mailto:ilaria.billato@phd.unipd.it">Ilaria Billato</a> </p>
<p>Martin Morgan, Sonali Arora, Lori Shepherd, <a href="mailto:davide.risso@unipd.it">Davide Risso</a>, <a href="mailto:ilaria.billato@unipd.it">Ilaria Billato</a> </p>
</div>
</div>

Expand Down Expand Up @@ -422,7 +422,6 @@ <h2 class="anchored" data-anchor-id="iranges-and-granges"><em>IRanges</em> and <

Extends:
Class "GenomicRanges", directly
Class "GRanges_OR_NULL", directly
Class "Ranges", by class "GenomicRanges", distance 2
Class "GenomicRanges_OR_missing", by class "GenomicRanges", distance 2
Class "GenomicRanges_OR_GenomicRangesList", by class "GenomicRanges", distance 2
Expand Down Expand Up @@ -667,8 +666,8 @@ <h2 class="anchored" data-anchor-id="biostrings-dna-or-amino-acid-sequences"><em
<span id="cb46-3"><a href="#cb46-3" aria-hidden="true" tabindex="-1"></a>chr14_dna <span class="ot">&lt;-</span> <span class="fu">getSeq</span>(Hsapiens, chr14_range)</span>
<span id="cb46-4"><a href="#cb46-4" aria-hidden="true" tabindex="-1"></a><span class="fu">letterFrequency</span>(chr14_dna, <span class="st">"GC"</span>, <span class="at">as.prob=</span><span class="cn">TRUE</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<div class="cell-output cell-output-stdout">
<pre><code> G|C
[1,] 0.336276</code></pre>
<pre><code> G|C
[1,] 0.3454924</code></pre>
</div>
</div>
<p><strong>Exercises</strong></p>
Expand Down Expand Up @@ -1334,18 +1333,23 @@ <h2 class="anchored" data-anchor-id="session-info">Session Info</h2>
<div class="code-copy-outer-scaffold"><div class="sourceCode cell-code" id="cb118"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb118-1"><a href="#cb118-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sessionInfo</span>()</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<div class="cell-output cell-output-stdout">
<pre><code>R version 4.6.0 (2026-04-24)
Platform: aarch64-apple-darwin23
Running under: macOS Tahoe 26.4.1
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.4 LTS

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 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
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Berlin
tzcode source: internal
time zone: Europe/Rome
tzcode source: system (glibc)

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
Expand All @@ -1371,60 +1375,58 @@ <h2 class="anchored" data-anchor-id="session-info">Session Info</h2>
[17] rtracklayer_1.72.0
[18] BiocIO_1.22.0
[19] GenomeInfoDb_1.48.0
[20] pwalign_1.8.0
[21] GenomicRanges_1.64.0
[22] Biostrings_2.80.0
[23] Seqinfo_1.2.0
[24] XVector_0.52.0
[25] IRanges_2.46.0
[26] S4Vectors_0.50.0
[27] BiocGenerics_0.58.0
[28] generics_0.1.4
[29] BiocStyle_2.40.0
[20] GenomicRanges_1.64.0
[21] Biostrings_2.80.0
[22] Seqinfo_1.2.0
[23] XVector_0.52.0
[24] IRanges_2.46.0
[25] S4Vectors_0.50.1
[26] BiocGenerics_0.58.1
[27] generics_0.1.4

loaded via a namespace (and not attached):
[1] DBI_1.3.0 bitops_1.0-9
[3] httr2_1.2.2 rlang_1.2.0
[5] magrittr_2.0.5 gypsum_1.8.0
[7] compiler_4.6.0 RSQLite_2.4.6
[9] png_0.1-9 vctrs_0.7.3
[11] ProtGenerics_1.44.0 pkgconfig_2.0.3
[13] crayon_1.5.3 fastmap_1.2.0
[15] dbplyr_2.5.2 rmarkdown_2.31
[17] UCSC.utils_1.8.0 scRNAseq_2.26.0
[19] purrr_1.2.2 bit_4.6.0
[21] xfun_0.57 cachem_1.1.0
[23] cigarillo_1.2.0 jsonlite_2.0.0
[25] blob_1.3.0 rhdf5filters_1.24.0
[27] DelayedArray_0.38.1 Rhdf5lib_2.0.0
[29] parallel_4.6.0 R6_2.6.1
[31] Rcpp_1.1.1-1.1 knitr_1.51
[33] Matrix_1.7-5 tidyselect_1.2.1
[35] rstudioapi_0.18.0 abind_1.4-8
[37] yaml_2.3.12 codetools_0.2-20
[39] curl_7.1.0 lattice_0.22-9
[41] alabaster.sce_1.12.0 tibble_3.3.1
[43] withr_3.0.2 KEGGREST_1.52.0
[45] evaluate_1.0.5 BiocFileCache_3.2.0
[47] alabaster.schemas_1.12.0 ExperimentHub_3.2.0
[49] pillar_1.11.1 BiocManager_1.30.27
[51] filelock_1.0.3 RCurl_1.98-1.18
[53] BiocVersion_3.23.1 ensembldb_2.36.0
[55] alabaster.base_1.13.0 alabaster.ranges_1.12.0
[57] glue_1.8.1 alabaster.matrix_1.12.0
[59] lazyeval_0.2.3 tools_4.6.0
[61] AnnotationHub_4.2.0 XML_3.99-0.23
[63] rhdf5_2.56.0 grid_4.6.0
[65] SingleCellExperiment_1.34.0 HDF5Array_1.40.0
[67] restfulr_0.0.16 cli_3.6.6
[69] rappdirs_0.3.4 S4Arrays_1.12.0
[71] dplyr_1.2.1 AnnotationFilter_1.36.0
[73] alabaster.se_1.12.0 digest_0.6.39
[75] SparseArray_1.12.2 rjson_0.2.23
[77] htmlwidgets_1.6.4 memoise_2.0.1
[79] htmltools_0.5.9 lifecycle_1.0.5
[81] h5mread_1.4.0 httr_1.4.8
[83] bit64_4.8.0 </code></pre>
[5] magrittr_2.0.5 otel_0.2.0
[7] gypsum_1.8.0 compiler_4.6.0
[9] RSQLite_3.52.0 png_0.1-9
[11] vctrs_0.7.3 ProtGenerics_1.44.0
[13] pkgconfig_2.0.3 crayon_1.5.3
[15] fastmap_1.2.0 dbplyr_2.5.2
[17] rmarkdown_2.31 UCSC.utils_1.8.0
[19] scRNAseq_2.26.0 purrr_1.2.2
[21] bit_4.6.0 xfun_0.57
[23] cachem_1.1.0 cigarillo_1.2.0
[25] jsonlite_2.0.0 blob_1.3.0
[27] rhdf5filters_1.24.0 DelayedArray_0.38.1
[29] Rhdf5lib_2.0.0 parallel_4.6.0
[31] R6_2.6.1 Rcpp_1.1.1-1.1
[33] knitr_1.51 Matrix_1.7-5
[35] tidyselect_1.2.1 rstudioapi_0.18.0
[37] abind_1.4-8 yaml_2.3.12
[39] codetools_0.2-20 curl_7.1.0
[41] lattice_0.22-9 alabaster.sce_1.12.0
[43] tibble_3.3.1 withr_3.0.2
[45] KEGGREST_1.52.0 evaluate_1.0.5
[47] BiocFileCache_3.2.0 alabaster.schemas_1.12.0
[49] ExperimentHub_3.2.0 pillar_1.11.1
[51] BiocManager_1.30.27 filelock_1.0.3
[53] RCurl_1.98-1.18 BiocVersion_3.23.1
[55] ensembldb_2.36.0 alabaster.base_1.12.0
[57] glue_1.8.1 alabaster.ranges_1.12.0
[59] alabaster.matrix_1.12.0 lazyeval_0.2.3
[61] tools_4.6.0 AnnotationHub_4.2.0
[63] XML_3.99-0.23 rhdf5_2.56.0
[65] grid_4.6.0 SingleCellExperiment_1.34.0
[67] HDF5Array_1.40.0 restfulr_0.0.16
[69] cli_3.6.6 rappdirs_0.3.4
[71] S4Arrays_1.12.0 dplyr_1.2.1
[73] AnnotationFilter_1.36.0 alabaster.se_1.12.0
[75] digest_0.6.39 SparseArray_1.12.2
[77] rjson_0.2.23 htmlwidgets_1.6.4
[79] memoise_2.0.1 htmltools_0.5.9
[81] lifecycle_1.0.5 h5mread_1.4.0
[83] httr_1.4.8 bit64_4.8.0 </code></pre>
</div>
</div>
</section>
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---
title: "Lab 1.4: Representations for biomolecular sequences"
author: Martin Morgan, Sonali Arora, Lori Shepherd, [Davide Risso](mailto:davide.risso@unipd.it), [Ilaria Billato](mailto:ilaria.billato@phd.unipd.it)
author: Martin Morgan, Sonali Arora, Lori Shepherd, [Davide Risso](mailto:davide.risso@unipd.it), [Ilaria Billato](mailto:ilaria.billato@unipd.it)
date: 25 May 2026
format:
html:
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4 changes: 2 additions & 2 deletions intro-to-r-bioc/L1.5-bioc-annotation.Rmd
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**Original Authors:** Martin Morgan, Sonali Arora, Lori Shepherd<br />
**Presenting Author:** [Davide Risso][], [Ilaria Billato][]</br >
**Date:** 6-11 July, 2025</br >
**Date:** 24-29 May, 2026</br >
**Back:** [Monday labs](lab-1-intro-to-r-bioc.html)

[Davide Risso]: mailto: davide.risso@unipd.it
[Ilaria Billato]: mailto: ilaria.billato@phd.unipd.it
[Ilaria Billato]: mailto: ilaria.billato@unipd.it


**Objective**: Learn about _Bioconductor_ resources for gene and
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