Last updated: 2018-06-26

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    File Version Author Date Message
    Rmd 789d8ef Briana Mittleman 2018-06-26 start test macs analysis. download package

In this analysis I want to test macs2 as a potential peak caller in the 3’ seq data. This is a widely used peak caller for chip seq data.

I have to create a specific environment to install macs2 because you need to use python 2.7. I call it macs-env. To access this environment I use source activate macs-env.

Session information

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.0.1   Rcpp_0.12.17      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.21.0      magrittr_1.5      evaluate_0.10.1  
[10] stringi_1.2.2     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.6.0     rmarkdown_1.8.5   tools_3.4.2      
[16] stringr_1.3.1     yaml_2.1.19       compiler_3.4.2   
[19] htmltools_0.3.6   knitr_1.18

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