Last updated: 2022-06-15

Checks: 7 0

Knit directory: rotation2/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

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.

Seed: set.seed(20220607)

The command set.seed(20220607) 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.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: d999122

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 d999122. 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: 


Unstaged changes:
    Modified:   .RData
    Modified:   .Rhistory

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.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/project_2.Rmd) and HTML (docs/project_2.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html 0aff555 chenh19 2022-06-15 Build site.
html a4e1e73 chenh19 2022-06-15 Build site.
html f0e98f9 chenh19 2022-06-14 Build site.
html eafa16b chenh19 2022-06-14 Build site.
html dfd60ce chenh19 2022-06-14 Build site.
Rmd 49f1922 chenh19 2022-06-14 wflow_publish("./analysis/*.Rmd")
html fd7271e chenh19 2022-06-14 Build site.
html 1b4d12e chenh19 2022-06-14 Build site.
html a6c402d chenh19 2022-06-14 Build site.
html cedad99 chenh19 2022-06-14 Build site.
html e3b9788 chenh19 2022-06-14 Build site.
html aed5eed chenh19 2022-06-14 Build site.
html 45bb6ed chenh19 2022-06-14 Build site.
html c23765a chenh19 2022-06-14 Build site.
Rmd 1277c93 chenh19 2022-06-14 wflow_publish("analysis/*.Rmd")
html b5fb71c chenh19 2022-06-14 Build site.
html 152325b chenh19 2022-06-14 Build site.
html 543ef4c chenh19 2022-06-14 Build site.
html 9b6cb27 chenh19 2022-06-14 Build site.
html 8674c8a chenh19 2022-06-14 Build site.
html ada4068 chenh19 2022-06-14 Build site.
html 0d08121 chenh19 2022-06-14 Build site.
html dd2046d chenh19 2022-06-14 Build site.
html 2c4cab1 chenh19 2022-06-14 Build site.
html d46eaab chenh19 2022-06-14 Build site.
html 02a0c26 chenh19 2022-06-14 Build site.
html abad46e chenh19 2022-06-14 Build site.
html 741027b chenh19 2022-06-14 Build site.
html bb15812 chenh19 2022-06-14 Build site.
html 93a27ae chenh19 2022-06-14 Build site.
html 27121a9 chenh19 2022-06-14 Build site.
Rmd fce1ffd chenh19 2022-06-14 wflow_publish("analysis/*.Rmd")
html 44517c1 chenh19 2022-06-13 Build site.
html da08f11 chenh19 2022-06-13 Build site.
html 572f6ba chenh19 2022-06-13 Build site.
html b8870d3 chenh19 2022-06-13 Build site.
html 719925e chenh19 2022-06-13 Build site.
html e7541fa chenh19 2022-06-13 Build site.
html 9d9615d chenh19 2022-06-13 Build site.
html bbd8978 chenh19 2022-06-13 Build site.
html e5a5b52 chenh19 2022-06-13 Build site.
Rmd c43ae1f chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
html 4d8bd72 chenh19 2022-06-13 Build site.
html 3373521 chenh19 2022-06-13 Build site.
html af21ea8 chenh19 2022-06-13 Build site.
Rmd 6e56d75 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
html f653f7b chenh19 2022-06-13 Build site.
html d69c892 chenh19 2022-06-13 Build site.
html 34d877d chenh19 2022-06-13 Build site.
html e72400b chenh19 2022-06-13 Build site.
html c411223 chenh19 2022-06-13 Build site.
html 1daccd2 chenh19 2022-06-13 Build site.
Rmd 63f46d2 chenh19 2022-06-13 wflow_publish("analysis/*.Rmd")
html 26adb45 chenh19 2022-06-13 Build site.
html a6022a8 chenh19 2022-06-13 Build site.
html 9abc4b8 chenh19 2022-06-13 Build site.
html f18d385 chenh19 2022-06-13 Build site.
html e991f56 chenh19 2022-06-13 Build site.
html 3c9b1d9 chenh19 2022-06-13 Build site.
html 34e0d02 chenh19 2022-06-13 Build site.
html 9be31af chenh19 2022-06-13 Build site.
html 0f41de8 chenh19 2022-06-13 Build site.
html 31ad035 chenh19 2022-06-13 Build site.
html bdf3b44 chenh19 2022-06-13 Build site.
html 8d0890c chenh19 2022-06-13 Build site.
Rmd 26f455b chenh19 2022-06-13 update
html 26f455b chenh19 2022-06-13 update

1. Understand SCEPTRE

a. Read the paper

Barry et al. 2021: SCEPTRE

First, SCEPTRE fits a negative binomial distribution to measure the effect of a single gRNA on a given gene via Z-score. Then, the distribution of gRNAs to cells is randomly sampled to build a gRNA-specific null distribution, recomputing a negative binomial Z-score. A skew-t distribution is fit to compare the test Z-score and the null distribution, and a two-sided p-value is derived, allowing for significance tests of increased or decreased gene expression.

From Morris et al. 2021: STING-Seq

c. Install the package

sudo -i R
install.packages("devtools")
devtools::install_github("katsevich-lab/sceptre")
q()

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     bslib_0.3.1      compiler_4.2.0   pillar_1.7.0    
 [5] later_1.3.0      git2r_0.30.1     jquerylib_0.1.4  tools_4.2.0     
 [9] getPass_0.2-2    digest_0.6.29    jsonlite_1.8.0   evaluate_0.15   
[13] tibble_3.1.7     lifecycle_1.0.1  pkgconfig_2.0.3  rlang_1.0.2     
[17] cli_3.3.0        rstudioapi_0.13  yaml_2.3.5       xfun_0.31       
[21] fastmap_1.1.0    httr_1.4.3       stringr_1.4.0    knitr_1.39      
[25] sass_0.4.1       fs_1.5.2         vctrs_0.4.1      rprojroot_2.0.3 
[29] glue_1.6.2       R6_2.5.1         processx_3.6.0   fansi_1.0.3     
[33] rmarkdown_2.14   callr_3.7.0      magrittr_2.0.3   whisker_0.4     
[37] ps_1.7.0         promises_1.2.0.1 htmltools_0.5.2  ellipsis_0.3.2  
[41] httpuv_1.6.5     utf8_1.2.2       stringi_1.7.6    crayon_1.5.1