Last updated: 2024-09-02
Checks: 6 1
Knit directory: duplex_sequencing_screen/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown is untracked by Git. To know which version of the R
Markdown file created these results, you’ll want to first commit it to
the Git repo. If you’re still working on the analysis, you can ignore
this warning. When you’re finished, you can run
wflow_publish
to commit the R Markdown file and build the
HTML.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200402)
was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version b998df6. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish
or
wflow_git_commit
). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
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Click here to view BCRABL Imatinib heatmaps generated using CRISPR-cut libraries
Click here to view growth rates from mCherry-tagged mutant standards that were spiked-in with the DMS library in our functional screens. The growth rates from these mutants help us normalize the screen for dose-response.
Click here to view
imatinib resistance heatmap and look at analyses of replicate
correlations in our DMS screens.
Click here to
view initial kinase function analyses.
Click here to
view our analyses of imatinib resistance in the full ABL kinase. This
includes heatmaps, scatterplots, boxplots, waterfall plots, all
analyzing the imatinib resistance profile of the ABL kinase.
.
sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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_1.6.2 Rcpp_1.0.4.6 rprojroot_1.3-2 digest_0.6.25
[5] later_1.0.0 R6_2.4.1 backports_1.1.7 jsonlite_1.7.2
[9] git2r_0.27.1 magrittr_2.0.1 evaluate_0.14 stringi_1.7.5
[13] rlang_0.4.11 fs_1.4.1 promises_1.1.0 jquerylib_0.1.4
[17] bslib_0.3.1 rmarkdown_2.14 tools_4.0.0 stringr_1.4.0
[21] glue_1.4.1 httpuv_1.5.2 xfun_0.31 yaml_2.2.1
[25] fastmap_1.1.0 compiler_4.0.0 htmltools_0.5.2 knitr_1.28
[29] sass_0.4.1