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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Template</title>
<meta charset="utf-8" />
<meta name="author" content="Leonardo Collado-Torres" />
<meta name="date" content="2020-03-23" />
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-161558379-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-161558379-1');
</script>
<link rel="stylesheet" href="xaringan-themer.css" type="text/css" />
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
# <strong>Template</strong>
## Analyzing <strong>scRNA-seq</strong> data with <strong>Bioconductor</strong> for <strong>LCG-EJ-UNAM</strong> March 2020
### <a href="http://lcolladotor.github.io/">Leonardo Collado-Torres</a>
### 2020-03-23
---
class: inverse
.center[
<a href="https://bioconductor.org/"><img src="https://osca.bioconductor.org/cover.png" style="width: 30%"/></a>
<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.
<a href='https://clustrmaps.com/site/1b5pl' title='Visit tracker'><img src='//clustrmaps.com/map_v2.png?cl=ffffff&w=150&t=n&d=tq5q8216epOrQBSllNIKhXOHUHi-i38brzUURkQEiXw'/></a>
]
.footnote[ Download the materials for this course with `usethis::use_course('lcolladotor/osca_LIIGH_UNAM_2020')` or view online at [**lcolladotor.github.io/osca_LIIGH_UNAM_2020**](http://lcolladotor.github.io/osca_LIIGH_UNAM_2020).]
<style type="text/css">
/* From https://github.com/yihui/xaringan/issues/147 */
.scroll-output {
height: 80%;
overflow-y: scroll;
}
/* https://stackoverflow.com/questions/50919104/horizontally-scrollable-output-on-xaringan-slides */
pre {
max-width: 100%;
overflow-x: scroll;
}
/* From https://github.com/yihui/xaringan/wiki/Font-Size */
.tiny{
font-size: 40%
}
/* From https://github.com/yihui/xaringan/wiki/Title-slide */
.title-slide {
background-image: url(https://raw.githubusercontent.com/Bioconductor/OrchestratingSingleCellAnalysis/master/images/Workflow.png);
background-size: 33%;
background-position: 0% 100%
}
</style>
---
class: middle
.center[
# Thanks!
Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan) and themed with [**xaringanthemer**](https://github.com/gadenbuie/xaringanthemer).
This course is based on the book [**Orchestrating Single Cell Analysis with Bioconductor**](https://osca.bioconductor.org/) by [Aaron Lun](https://www.linkedin.com/in/aaron-lun-869b5894/), [Robert Amezquita](https://robertamezquita.github.io/), [Stephanie Hicks](https://www.stephaniehicks.com/) and [Raphael Gottardo](http://rglab.org), plus [**WEHI's scRNA-seq course**](https://drive.google.com/drive/folders/1cn5d-Ey7-kkMiex8-74qxvxtCQT6o72h) by [Peter Hickey](https://www.peterhickey.org/).
You can find the files for this course at [lcolladotor/osca_LIIGH_UNAM_2020](https://github.com/lcolladotor/osca_LIIGH_UNAM_2020).
Instructor: [**Leonardo Collado-Torres**](http://lcolladotor.github.io/).
<a href="https://www.libd.org"><img src="img/LIBD_logo.jpg" style="width: 20%" /></a>
]
.footnote[ Download the materials for this course with `usethis::use_course('lcolladotor/osca_LIIGH_UNAM_2020')` or view online at [**lcolladotor.github.io/osca_LIIGH_UNAM_2020**](http://lcolladotor.github.io/osca_LIIGH_UNAM_2020).]
---
# R session information
.scroll-output[
.tiny[
```r
options(width = 120)
sessioninfo::session_info()
```
```
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.3 (2020-02-29)
## os macOS Catalina 10.15.3
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-03-23
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date lib source
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
## cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.0)
## colorout * 1.2-1 2019-05-07 [1] Github (jalvesaq/colorout@7ea9440)
## crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
## digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0)
## evaluate 0.14 2019-05-28 [1] CRAN (R 3.6.0)
## fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0)
## glue 1.3.2 2020-03-12 [1] CRAN (R 3.6.0)
## htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.0)
## knitr 1.28 2020-02-06 [1] CRAN (R 3.6.0)
## magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
## Rcpp 1.0.4 2020-03-17 [1] CRAN (R 3.6.0)
## rlang 0.4.5 2020-03-01 [1] CRAN (R 3.6.0)
## rmarkdown 2.1 2020-01-20 [1] CRAN (R 3.6.0)
## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
## stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0)
## stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
## withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
## xaringan 0.15 2020-03-04 [1] CRAN (R 3.6.3)
## xaringanthemer * 0.2.0 2020-03-22 [1] Github (gadenbuie/xaringanthemer@460f441)
## xfun 0.12 2020-01-13 [1] CRAN (R 3.6.0)
## yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.0)
##
## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
```
]]
</textarea>
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// delete the temporary CSS (for displaying all slides initially) when the user
// starts to view slides
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var deleted = false;
slideshow.on('beforeShowSlide', function(slide) {
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/* Replace <script> tags in slides area to make them executable
*
* Runs after post-processing of markdown source into slides and replaces only
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var scripts = document.querySelectorAll(
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const preParents = [];
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