Chapter 4 Practicing with Genomic Data

We will use the data from this portal: https://portal.gdc.cancer.gov/

4.1 Installing the R package

You can find use the R package here to get these data: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html

4.2 Getting the data

Walk through the steps of how to obtain this data

4.3 Basic analyses

Walk through some basic analyses, referencing techniques from https://hutchdatascience.org/Choosing_Genomics_Tools/

4.4 Basic plots

sessionInfo()

## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 LTS
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## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
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## locale:
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## time zone: Etc/UTC
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## attached base packages:
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##  [1] digest_0.6.34    R6_2.5.1         bookdown_0.39.1  fastmap_1.1.1   
##  [5] xfun_0.44.4      cachem_1.0.8     knitr_1.47.3     htmltools_0.5.7 
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## [13] jquerylib_0.1.4  compiler_4.3.2   tools_4.3.2      evaluate_0.23   
## [17] bslib_0.6.1      yaml_2.3.8       rlang_1.1.4      jsonlite_1.8.8