diff --git a/README.md b/README.md index ffd4726..32fb7e6 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,8 @@ devtools::install_github("CSOgroup/select") If you use this tool, please cite the papers - Mina, M., Iyer, A., Tavernari, D., Raynaud, F., & Ciriello, G. (2020). [Discovering functional evolutionary dependencies in human cancers](https://www.nature.com/articles/s41588-020-0703-5) Nature Genetics, 52(11), 1198-1207. -- Mina, M., Raynaud, F., Tavernari, D., Battistello, E., Sungalee, S., Saghafinia, S., ... & Ciriello, G. (2017). [Conditional selection of genomic alterations dictates cancer evolution and oncogenic dependencies.](https://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30261-1) Cancer cell, 32(2), 155-168. + +- Mina, Marco and Raynaud, Franck and Tavernari, Daniele and Battistello, Elena and Sungalee, Stephanie and Saghafinia, Sadegh and Laessle, Titouan and Sanchez-Vega, Francisco and Schultz, Nikolaus and Oricchio, Elisa and Ciriello, G. (2017). [Conditional selection of genomic alterations dictates cancer evolution and oncogenic dependencies.](https://www.cell.com/cancer-cell/fulltext/S1535-6108(17)30261-1) Cancer cell, 32(2), 155-168. ### Contribution guidelines ### diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html index f0e4cf0..f85ca04 100644 --- a/docs/articles/introduction.html +++ b/docs/articles/introduction.html @@ -206,35 +206,35 @@

Running select#> [1] "-> Parsing and Filtering GAM..." #> [1] "-> Generating null model..." #> user system elapsed -#> 3.323 0.006 3.328 +#> 3.362 0.006 3.368 #> [1] "Memory usage: 31.4 MB" #> [1] "-> Collecting event stats on observed GAM..." #> user system elapsed -#> 0.119 0.389 0.031 +#> 0.104 0.229 0.023 #> [1] "Memory usage: 31.6 MB" #> [1] "-> Calculating wMI on observed GAM..." #> user system elapsed -#> 0.034 0.000 0.033 +#> 0.025 0.000 0.024 #> [1] "Memory usage: 32.1 MB" #> [1] "-> Collecting event stats on null model..." #> user system elapsed -#> 7.286 22.550 1.480 +#> 9.555 31.501 2.059 #> [1] "Memory usage: 37.4 MB" #> [1] "-> Comparing observed GAM vs null model..." #> user system elapsed -#> 1.049 0.001 1.049 +#> 1.018 0.000 1.018 #> [1] "Memory usage: 38 MB" #> [1] "-> Calculating wMI on null model..." #> user system elapsed -#> 1.555 0.007 1.561 +#> 1.692 0.006 1.698 #> [1] "Memory usage: 59.8 MB" #> [1] "-> Calculating P-value based on wMI..." #> user system elapsed -#> 0.024 0.009 0.034 +#> 0.029 0.002 0.031 #> [1] "Memory usage: 60 MB" #> [1] "-> Deriving average background wMI..." #> user system elapsed -#> 0.949 0.001 0.949 +#> 0.91 0.00 0.91 #> [1] "Memory usage: 60.3 MB" #> [1] "-> Building results table..." #> [1] "-> Calculating APC score..." @@ -244,13 +244,13 @@

Running select#> [1] "Not correcting with APC as there are not enough interactions to estimate the background distribution. Uncorrected scores will be used." #> [1] "Not correcting with APC as there are not enough interactions to estimate the background distribution. Uncorrected scores will be used." #> user system elapsed -#> 0.203 0.000 0.202 +#> 0.201 0.000 0.201 #> [1] "Memory usage: 64.1 MB" #> [1] "-> Performing wMI FDR analysis..." #> Warning in rbind(deparse.level, ...): number of columns of result, 7, is not a #> multiple of vector length 6 of arg 2 #> user system elapsed -#> 3.879 0.044 3.923 +#> 3.819 0.024 3.843 #> [1] "Memory usage: 64.3 MB" #> [1] "-> Calculating APC threshold..." diff --git a/docs/index.html b/docs/index.html index f612ddf..bb5f858 100644 --- a/docs/index.html +++ b/docs/index.html @@ -86,7 +86,7 @@

What is this repository for? @@ -102,6 +102,7 @@

How To
  • How to use
    • Check the introduction fom vignettes folder or the website.
      • +
    • Also refere to methods section of papers to know the best way to apply the method.
    • @@ -111,16 +112,16 @@

    Citation

    If you use this tool, please cite the papers

    Contribution guidelines

      -
    • SELECT was originally developed by Marco Mina at the University of Lausanne, Switzerland.
      • -
    • SELECT is currently maintained by Arvind Iyer from the Computational Systems Oncology lab (CSO) at the University of Lausanne (Unil), Switzerland.
      • +
    • SELECT was originally developed by Marco Mina at the University of Lausanne, Switzerland.
      • +
    • SELECT is currently maintained by Arvind Iyer and memeber of the Computational Systems Oncology lab (CSO) at the University of Lausanne (Unil), Switzerland.
    diff --git a/docs/news/index.html b/docs/news/index.html index a83e64c..d6a997f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -57,6 +57,10 @@

    Changelog

    Source: NEWS.md
    +
    +

    select 1.6.4

    +
    • Fixed some bugs and updated code.
      • +

    select 1.6.3

    • Added a NEWS.md file to track changes to the package.
      • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 0067917..f50bad9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: introduction: introduction.html -last_built: 2024-11-26T12:45Z +last_built: 2024-11-26T13:16Z