class: center, middle, inverse, title-slide # <strong>Spatial Transcriptomics</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.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 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 ``` ]]