Data Integration

Analyzing scRNA-seq data with Bioconductor for LCG-EJ-UNAM March 2020

Leonardo Collado-Torres

2020-03-22

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This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

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.

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Thanks!

Slides created via the R package xaringan and themed with xaringanthemer.

This course is based on the book Orchestrating Single Cell Analysis with Bioconductor by Aaron Lun, Robert Amezquita, Stephanie Hicks and Raphael Gottardo, plus WEHI's scRNA-seq course by Peter Hickey.

You can find the files for this course at lcolladotor/osca_LIIGH_UNAM_2020.

Instructor: Leonardo Collado-Torres.

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.

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R session informationoptions(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
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Data Integration

Analyzing scRNA-seq data with Bioconductor for LCG-EJ-UNAM March 2020

Leonardo Collado-Torres

2020-03-22

Thanks!

R session information

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