Last updated: 2024-05-28

Checks: 7 0

Knit directory: PPP/

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    Ignored:    output/TieDIE/input/.DS_Store
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File Version Author Date Message
html da0867e Zhen Zuo 2024-05-28 Build site.
html 5de8ce9 Zhen Zuo 2024-05-28 Build site.
Rmd 3d1adad Zhen Zuo 2024-05-28 Publish files
html 896cebd Zhen Zuo 2024-05-28 Build site.
Rmd ab5880c Zhen Zuo 2024-05-28 Publish files

TieDIE was first featured in the 2013 Nature paper “Comprehensive molecular characterization of clear cell renal cell carcinoma”. In this TCGA (The Cancer Genome Atlas) network publication, a TieDIE analysis was used to connnect frequently mutated genes involving the SWI/SNF chromatin remodelling complex to a diverse set of gene expression changes characteristic of tumor development and progression. The TieDIE manuscript was not yet published at the time of the Nature publication and so is cited by name and author only. The TieDIE network solution is shown in figure 4 of the main text, which can be found at this link: http://www.nature.com/nature/journal/v499/n7456/full/nature12222.html .

Run TieDIE

result:
    python ../../bin/tiedie -u upstream.input -d downstream.input -n pathway.sif -s 1.0


sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       httr_1.4.7        cli_3.6.2         knitr_1.46       
 [5] rlang_1.1.3       xfun_0.44         stringi_1.8.4     processx_3.8.4   
 [9] promises_1.3.0    jsonlite_1.8.8    glue_1.7.0        rprojroot_2.0.4  
[13] git2r_0.33.0      htmltools_0.5.8.1 httpuv_1.6.15     ps_1.7.6         
[17] sass_0.4.9        fansi_1.0.6       rmarkdown_2.27    jquerylib_0.1.4  
[21] tibble_3.2.1      evaluate_0.23     fastmap_1.2.0     yaml_2.3.8       
[25] lifecycle_1.0.4   whisker_0.4.1     stringr_1.5.1     compiler_4.4.0   
[29] fs_1.6.4          pkgconfig_2.0.3   Rcpp_1.0.12       rstudioapi_0.16.0
[33] later_1.3.2       digest_0.6.35     R6_2.5.1          utf8_1.2.4       
[37] pillar_1.9.0      callr_3.7.6       magrittr_2.0.3    bslib_0.7.0      
[41] tools_4.4.0       cachem_1.1.0      getPass_0.2-4