-
Notifications
You must be signed in to change notification settings - Fork 3
/
11-multi-sample-comparisons.html
308 lines (264 loc) · 13.6 KB
/
11-multi-sample-comparisons.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Multi-Sample Comparisons</title>
<meta charset="utf-8" />
<meta name="author" content="Leonardo Collado-Torres" />
<meta name="date" content="2020-03-22" />
<!-- 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>Multi-Sample Comparisons</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>
### 2020-03-22
---
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.github.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 RStudio
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-03-22
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date lib source
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
## backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0)
## callr 3.4.2 2020-02-12 [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)
## desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
## devtools * 2.2.2 2020-02-17 [1] CRAN (R 3.6.0)
## digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.0)
## ellipsis 0.3.0 2019-09-20 [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)
## fs 1.3.2 2020-03-05 [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)
## memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
## packrat 0.5.0 2018-11-14 [1] CRAN (R 3.6.0)
## pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0)
## pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.2)
## processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.0)
## ps 1.3.2 2020-02-13 [1] CRAN (R 3.6.0)
## R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
## Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.0)
## remotes 2.1.1 2020-02-15 [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)
## rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
## rsconnect 0.8.16 2019-12-13 [1] CRAN (R 3.6.2)
## rstudioapi 0.11 2020-02-07 [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)
## testthat * 2.3.2 2020-03-02 [1] CRAN (R 3.6.2)
## usethis * 1.5.1 2019-07-04 [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>
<style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
<script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
<script>var slideshow = remark.create({
"highlightStyle": "github",
"highlightLines": true,
"countIncrementalSlides": false
});
if (window.HTMLWidgets) slideshow.on('afterShowSlide', function (slide) {
window.dispatchEvent(new Event('resize'));
});
(function(d) {
var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
if (!r) return;
s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
d.head.appendChild(s);
})(document);
(function(d) {
var el = d.getElementsByClassName("remark-slides-area");
if (!el) return;
var slide, slides = slideshow.getSlides(), els = el[0].children;
for (var i = 1; i < slides.length; i++) {
slide = slides[i];
if (slide.properties.continued === "true" || slide.properties.count === "false") {
els[i - 1].className += ' has-continuation';
}
}
var s = d.createElement("style");
s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
d.head.appendChild(s);
})(document);
// delete the temporary CSS (for displaying all slides initially) when the user
// starts to view slides
(function() {
var deleted = false;
slideshow.on('beforeShowSlide', function(slide) {
if (deleted) return;
var sheets = document.styleSheets, node;
for (var i = 0; i < sheets.length; i++) {
node = sheets[i].ownerNode;
if (node.dataset["target"] !== "print-only") continue;
node.parentNode.removeChild(node);
}
deleted = true;
});
})();
(function() {
"use strict"
/* Replace <script> tags in slides area to make them executable
*
* Runs after post-processing of markdown source into slides and replaces only
* <script>s on the last slide of continued slides using the .has-continuation
* class added by xaringan. Finally, any <script>s in the slides area that
* aren't executed are commented out.
*/
var scripts = document.querySelectorAll(
'.remark-slides-area .remark-slide-container:not(.has-continuation) script'
);
if (!scripts.length) return;
for (var i = 0; i < scripts.length; i++) {
var s = document.createElement('script');
var code = document.createTextNode(scripts[i].textContent);
s.appendChild(code);
scripts[i].parentElement.replaceChild(s, scripts[i]);
}
var scriptsNotExecuted = document.querySelectorAll(
'.remark-slides-area .remark-slide-container.has-continuation script'
);
if (!scriptsNotExecuted.length) return;
for (var i = 0; i < scriptsNotExecuted.length; i++) {
var comment = document.createComment(scriptsNotExecuted[i].outerHTML)
scriptsNotExecuted[i].parentElement.replaceChild(comment, scriptsNotExecuted[i])
}
})();
(function() {
var links = document.getElementsByTagName('a');
for (var i = 0; i < links.length; i++) {
if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
links[i].target = '_blank';
}
}
})();
// adds .remark-code-has-line-highlighted class to <pre> parent elements
// of code chunks containing highlighted lines with class .remark-code-line-highlighted
(function(d) {
const hlines = d.querySelectorAll('.remark-code-line-highlighted');
const preParents = [];
const findPreParent = function(line, p = 0) {
if (p > 1) return null; // traverse up no further than grandparent
const el = line.parentElement;
return el.tagName === "PRE" ? el : findPreParent(el, ++p);
};
for (let line of hlines) {
let pre = findPreParent(line);
if (pre && !preParents.includes(pre)) preParents.push(pre);
}
preParents.forEach(p => p.classList.add("remark-code-has-line-highlighted"));
})(document);</script>
<script>
slideshow._releaseMath = function(el) {
var i, text, code, codes = el.getElementsByTagName('code');
for (i = 0; i < codes.length;) {
code = codes[i];
if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
text = code.textContent;
if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
/^\$\$(.|\s)+\$\$$/.test(text) ||
/^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
code.outerHTML = code.innerHTML; // remove <code></code>
continue;
}
}
i++;
}
};
slideshow._releaseMath(document);
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement('script');
script.type = 'text/javascript';
script.src = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
if (location.protocol !== 'file:' && /^https?:/.test(script.src))
script.src = script.src.replace(/^https?:/, '');
document.getElementsByTagName('head')[0].appendChild(script);
})();
</script>
</body>
</html>