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01-introduction.html
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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Introducción</title>
<meta charset="utf-8" />
<meta name="author" content="Leonardo Collado-Torres" />
<meta name="date" content="2020-08-03" />
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class: center, middle, inverse, title-slide
# <strong>Introducción</strong>
## <strong>Bioconductor</strong> para datos transcriptómicos de célula única (<strong>scRNA-seq</strong>) – <strong>CDSB2020</strong>
### <a href="http://lcolladotor.github.io/">Leonardo Collado-Torres</a>
### 2020-08-03
---
class: inverse
.center[
<a href="https://osca.bioconductor.org/"><img src="https://raw.githubusercontent.com/Bioconductor/OrchestratingSingleCellAnalysis-release/master/images/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=rP3KLyAMuzVNcJFL-_C-B0XnLNVy8Sp6a8HDaKEnSzc'/></a>
]
.footnote[Descarga los materiales con `usethis::use_course('comunidadbioinfo/cdsb2020')` o revisalos en línea vía [**comunidadbioinfo.github.io/cdsb2020**](http://comunidadbioinfo.github.io/cdsb2020).]
<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>
---
# Orígenes del curso
--
* El libro [**Orchestrating Single Cell Analysis With Bioconductor**](ohttps://osca.bioconductor.org/) escrito por [Aaron Lun](https://www.linkedin.com/in/aaron-lun-869b5894/), [Robert Amezquita](https://robertamezquita.github.io/), [Stephanie Hicks](https://www.stephaniehicks.com/) y [Raphael Gottardo](http://rglab.org)
--
Amezquita, R.A., Lun, A.T.L., Becht, E. et al. Orchestrating single-cell analysis with Bioconductor. _Nat Methods_ 17, 137–145 (2020). DOI: [10.1038/s41592-019-0654-x](https://doi.org/10.1038/s41592-019-0654-x)
--
* [**Curso de scRNA-seq de WEHI**](https://drive.google.com/drive/folders/1cn5d-Ey7-kkMiex8-74qxvxtCQT6o72h) creado por [Peter Hickey](https://www.peterhickey.org/)
---
class: center, middle
# Instructor
**Leonardo Collado-Torres**
<img src="http://lcolladotor.github.io/authors/admin/avatar_hub730ffb954e879fe0ab174cacb839b41_1326712_270x270_fill_lanczos_center_2.png" />
* Sitio web: [lcolladotor.github.io](http://lcolladotor.github.io)
* Twitter: [fellgernon](https://twitter.com/fellgernon)
---
background-image: url(img/01-intro/Slide1.png)
background-size: 100%
---
background-image: url(img/01-intro/Slide2.png)
background-size: 100%
---
background-image: url(img/01-intro/Slide3.png)
background-size: 100%
---
background-image: url(img/01-intro/Slide4.png)
background-size: 100%
---
# Pre-requisitos
.scroll-output[
Instala R 4.0.x desde [CRAN](https://cran.r-project.org/) y luego instala los siguientes paquetes de R:
```r
## Para instalar paquetes de Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## Instala los paquetes de R que necesitamos
BiocManager::install(
c(
'SingleCellExperiment',
'usethis',
'here',
'scran',
'scater',
'scRNAseq',
'org.Mm.eg.db',
'AnnotationHub',
'ExperimentHub',
'BiocFileCache',
'DropletUtils',
'EnsDb.Hsapiens.v86',
'TENxPBMCData',
'BiocSingular',
'batchelor',
'uwot',
'Rtsne',
'pheatmap',
'fossil',
'ggplot2',
'cowplot',
'RColorBrewer',
'plotly',
'iSEE',
'pryr',
'spatialLIBD',
'sessioninfo'
)
)
```
Tabmién debes instalar [RStudio](https://rstudio.com/products/rstudio/download/#download) versión 1.3.1 o la más nueva de preferencia.
]
---
# Ayudantes del curso
* [Ana Betty Villaseñor Altamirano](https://twitter.com/AnaBetty2304)
* [Aurora Labastida](https://twitter.com/alabasti1)
* [Carlos Gabriel Aguilar Pérez](https://twitter.com/Carlos_Aplysia)
---
# Materiales del curso
--
* Descargalos con `usethis::use_course('comunidadbioinfo/cdsb2020')`
--
* Checalos en línea a través de [**comunidadbioinfo.github.io/cdsb2020**](http://comunidadbioinfo.github.io/cdsb2020)
--
* **Clone** el repositorio de GitHub, lo cual te hará más fácil el poder actualizar tus archivos con la versión más reciente usando *git pull*
```bash
## Si tienes las llaves de SSH configuradas
git clone [email protected]:comunidadbioinfo/cdsb2020.git
## o vía https
git clone https://github.com/comunidadbioinfo/cdsb2020.git
```
Desde R:
```r
git2r::clone('https://github.com/comunidadbioinfo/cdsb2020',
'csdb2020')
```
---
# Crea tu propio proyecto
Te recomiendo que crees tu propio proyecto y actives el control de versiones
```r
usethis::create_project('~/Desktop/cdsb2020_leo')
```
```r
## Crea un archivo de setup
usethis::use_r('00-setup.R')
```
---
En este script de setup, guarda los siguientes comandos
```r
## Crea el repositorio de Git
usethis::use_git()
## Utiliza GitHub
usethis::browse_github_token()
usethis::edit_r_environ() ## y después reinicia R
usethis::use_github() ## crea un commit, luego corre este comando
## Empieza tus notas sobre la introducción a scRNA-seq
usethis::use_r('01-introduction.R')
```
Ve el ejemplo en [**cdsb2020_leo**](https://github.com/lcolladotor/cdsb2020_leo)
---
# Pedir ayuda
--
* Usa la manita azul de Zoom: "raise your **hand**"
--
* Crea un **issue** en [cdsb2020](https://github.com/comunidadbioinfo/cdsb2020/issues). ¡Acuérdate de incluir un ejemplo reproducible!
--
* De forma más general, a través del [**Bioconductor Support Website**](https://support.bioconductor.org/) etiquetando el paquete de R relacionado.
--
* Algunos blog posts relacionados: [**How to ask for help for Bioconductor packages**](http://lcolladotor.github.io/2017/03/06/how-to-ask-for-help-for-bioconductor-packages/#.XnjLRNNKh0s), [**Asking for help is challenging but is typically worth it**](http://lcolladotor.github.io/2018/11/12/asking-for-help-is-challenging-but-is-typically-worth-it/#.XnjLf9NKh0s), y [**Learning from our search history**](http://lcolladotor.github.io/2020/02/12/learning-from-our-search-history/)
--
* La plática de [Jenny Bryan](https://twitter.com/JennyBryan) para `rstudio::conf(2020)`: [**Object of type ‘closure’ is not subsettable**](https://resources.rstudio.com/rstudio-conf-2020/object-of-type-closure-is-not-subsettable-jenny-bryan)
---
background-image: url(https://raw.githubusercontent.com/Bioconductor/OrchestratingSingleCellAnalysis-release/master/images/cover.png)
background-size: contain
---
background-image: url(https://raw.githubusercontent.com/Bioconductor/OrchestratingSingleCellAnalysis-release/master/images/SingleCellExperiment.png)
background-size: contain
---
background-image: url(https://raw.githubusercontent.com/Bioconductor/OrchestratingSingleCellAnalysis-release/master/images/Workflow.png)
background-size: contain
---
background-image: url(http://research.libd.org/spatialLIBD/reference/figures/README-access_data-1.png)
background-size: contain
---
# Introdución rápida: [OSCA](https://osca.bioconductor.org/overview.html#quick-start)
```r
library('scRNAseq')
library('scater')
library('scran')
library('plotly')
```
---
.scroll-output[
```r
sce <- scRNAseq::MacoskoRetinaData()
```
```
## snapshotDate(): 2020-04-27
```
```
## see ?scRNAseq and browseVignettes('scRNAseq') for documentation
```
```
## loading from cache
```
```
## see ?scRNAseq and browseVignettes('scRNAseq') for documentation
```
```
## loading from cache
```
```r
## ¿Qué tan grandes son los datos?
pryr::object_size(sce)
```
```
## Registered S3 method overwritten by 'pryr':
## method from
## print.bytes Rcpp
```
```
## 461 MB
```
```r
## ¿Cómo es el objeto?
sce
```
```
## class: SingleCellExperiment
## dim: 24658 49300
## metadata(0):
## assays(1): counts
## rownames(24658): KITL TMTC3 ... 1110059M19RIK GM20861
## rowData names(0):
## colnames(49300): r1_GGCCGCAGTCCG r1_CTTGTGCGGGAA ... p1_TAACGCGCTCCT
## p1_ATTCTTGTTCTT
## colData names(2): cell.id cluster
## reducedDimNames(0):
## altExpNames(0):
```
]
---
.scroll-output[
```r
# Control de calidad.
es.mito <- grepl("^MT-", rownames(sce))
qcstats <-
scater::perCellQCMetrics(sce, subsets = list(Mito = es.mito))
filtered <-
scater::quickPerCellQC(qcstats, percent_subsets = "subsets_Mito_percent")
sce <- sce[, !filtered$discard]
# Normalización.
sce <- scater::logNormCounts(sce)
# Selección de genes.
dec <- scran::modelGeneVar(sce)
hvg <- scran::getTopHVGs(dec, prop = 0.1)
# Reducción de dimensiones.
set.seed(1234)
sce <- scater::runPCA(sce, ncomponents = 25, subset_row = hvg)
sce <- scater::runUMAP(sce, dimred = 'PCA', external_neighbors = TRUE)
# Clustering.
g <- scran::buildSNNGraph(sce, use.dimred = 'PCA')
sce$clusters <- factor(igraph::cluster_louvain(g)$membership)
```
]
---
```r
# Visualización.
scater::plotUMAP(sce, colour_by = "clusters")
```
<!-- -->
---
```r
# Visualización interactiva.
p <- scater::plotUMAP(sce, colour_by = "clusters")
plotly::ggplotly(p)
```
---
class: middle
.center[
# ¡Gracias!
Las diapositivias fueron hechas con el paquete de R [**xaringan**](https://github.com/yihui/xaringan) y configuradas con [**xaringanthemer**](https://github.com/gadenbuie/xaringanthemer).
Este curso está basado en el libro [**Orchestrating Single Cell Analysis with Bioconductor**](https://osca.bioconductor.org/) de [Aaron Lun](https://www.linkedin.com/in/aaron-lun-869b5894/), [Robert Amezquita](https://robertamezquita.github.io/), [Stephanie Hicks](https://www.stephaniehicks.com/) y [Raphael Gottardo](http://rglab.org), además del [**curso de scRNA-seq para WEHI**](https://drive.google.com/drive/folders/1cn5d-Ey7-kkMiex8-74qxvxtCQT6o72h) creado por [Peter Hickey](https://www.peterhickey.org/).
Puedes encontrar los archivos para este taller en [comunidadbioinfo/cdsb2020](https://github.com/comunidadbioinfo/cdsb2020).
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[Descarga los materiales con `usethis::use_course('comunidadbioinfo/cdsb2020')` o revisalos en línea vía [**comunidadbioinfo.github.io/cdsb2020**](http://comunidadbioinfo.github.io/cdsb2020).]
---
# Detalles de la sesión de R
.scroll-output[
.tiny[
```r
options(width = 120)
sessioninfo::session_info()
```
```
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.2 (2020-06-22)
## os macOS Catalina 10.15.5
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-08-02
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date lib source
## AnnotationDbi 1.50.3 2020-07-25 [1] Bioconductor
## AnnotationHub 2.20.0 2020-04-27 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
## beeswarm 0.2.3 2016-04-25 [1] CRAN (R 4.0.0)
## Biobase * 2.48.0 2020-04-27 [1] Bioconductor
## BiocFileCache 1.12.0 2020-04-27 [1] Bioconductor
## BiocGenerics * 0.34.0 2020-04-27 [1] Bioconductor
## BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
## BiocNeighbors 1.6.0 2020-04-27 [1] Bioconductor
## BiocParallel 1.22.0 2020-04-27 [1] Bioconductor
## BiocSingular 1.4.0 2020-04-27 [1] Bioconductor
## BiocVersion 3.11.1 2020-04-07 [1] Bioconductor
## bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0)
## bit64 0.9-7.1 2020-07-15 [1] CRAN (R 4.0.2)
## bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
## blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
## cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
## codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2)
## colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681)
## colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
## cowplot 1.0.0 2019-07-11 [1] CRAN (R 4.0.0)
## crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
## curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
## data.table 1.13.0 2020-07-24 [1] CRAN (R 4.0.2)
## DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
## dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.2)
## DelayedArray * 0.14.1 2020-07-14 [1] Bioconductor
## DelayedMatrixStats 1.10.1 2020-07-03 [1] Bioconductor
## digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
## dplyr 1.0.0 2020-05-29 [1] CRAN (R 4.0.2)
## dqrng 0.2.1 2019-05-17 [1] CRAN (R 4.0.0)
## edgeR 3.30.3 2020-06-02 [1] Bioconductor
## ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
## evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
## ExperimentHub 1.14.0 2020-04-27 [1] Bioconductor
## fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
## farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
## fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.0)
## generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
## GenomeInfoDb * 1.24.2 2020-06-15 [1] Bioconductor
## GenomeInfoDbData 1.2.3 2020-04-16 [1] Bioconductor
## GenomicRanges * 1.40.0 2020-04-27 [1] Bioconductor
## ggbeeswarm 0.6.0 2017-08-07 [1] CRAN (R 4.0.0)
## ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
## glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
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## htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
## htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
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## httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
## igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.0)
## interactiveDisplayBase 1.26.3 2020-06-02 [1] Bioconductor
## IRanges * 2.22.2 2020-05-21 [1] Bioconductor
## irlba 2.3.3 2019-02-05 [1] CRAN (R 4.0.0)
## jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.0)
## knitr 1.29 2020-06-23 [1] CRAN (R 4.0.0)
## labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
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## limma 3.44.3 2020-06-12 [1] Bioconductor
## locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.0.0)
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## Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
## matrixStats * 0.56.0 2020-03-13 [1] CRAN (R 4.0.0)
## memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
## mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
## pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
## plotly * 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.0)
## promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2)
## pryr 0.1.4 2018-02-18 [1] CRAN (R 4.0.0)
## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
## R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
## rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0)
## Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
## RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0)
## rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
## rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.0)
## RSpectra 0.16-0 2019-12-01 [1] CRAN (R 4.0.0)
## RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0)
## rsvd 1.0.3 2020-02-17 [1] CRAN (R 4.0.0)
## S4Vectors * 0.26.1 2020-05-16 [1] Bioconductor
## scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
## scater * 1.16.2 2020-06-26 [1] Bioconductor
## scran * 1.16.0 2020-04-27 [1] Bioconductor
## scRNAseq * 2.2.0 2020-05-07 [1] Bioconductor
## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
## shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2)
## showtext 0.8-1 2020-05-25 [1] CRAN (R 4.0.2)
## showtextdb 3.0 2020-06-04 [1] CRAN (R 4.0.2)
## SingleCellExperiment * 1.10.1 2020-04-28 [1] Bioconductor
## statmod 1.4.34 2020-02-17 [1] CRAN (R 4.0.0)
## stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
## stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
## SummarizedExperiment * 1.18.2 2020-07-14 [1] Bioconductor
## sysfonts 0.8.1 2020-05-08 [1] CRAN (R 4.0.0)
## tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
## tidyr 1.1.0 2020-05-20 [1] CRAN (R 4.0.2)
## tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
## uwot 0.1.8 2020-03-16 [1] CRAN (R 4.0.0)
## vctrs 0.3.2 2020-07-15 [1] CRAN (R 4.0.2)
## vipor 0.4.5 2017-03-22 [1] CRAN (R 4.0.0)
## viridis 0.5.1 2018-03-29 [1] CRAN (R 4.0.0)
## viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)
## whisker 0.4 2019-08-28 [1] CRAN (R 4.0.0)
## withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
## xaringan 0.16 2020-03-31 [1] CRAN (R 4.0.0)
## xaringanthemer * 0.3.0 2020-05-04 [1] CRAN (R 4.0.0)
## xfun 0.16 2020-07-24 [1] CRAN (R 4.0.2)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0)
## XVector 0.28.0 2020-04-27 [1] Bioconductor
## yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
## zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
##
## [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
```
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