Last updated: 2024-09-19

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Knit directory: spatialsnippets/

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File Version Author Date Message
Rmd 511594f swbioinf 2024-09-19 wflow_publish("analysis/")
html 5347093 swbioinf 2024-09-17 Build site.
Rmd 7eec547 swbioinf 2024-09-17 wflow_publish("analysis/")
html 2383812 swbioinf 2024-08-23 Build site.
Rmd eba1dad swbioinf 2024-08-23 wflow_publish(c("analysis/e_template.Rmd", "analysis/index.Rmd"))

This is a loose template for making new examples. Adjust as needed.

Overview

A couple of paragraphs describing what this test is, why it is neccessary.

Citations formatted as (Phipson et al. 2022), and included in bibiliography json .bib file.

Include an image of what is being tested. Save it in docs/assets/, and link as below;

This requires:

  • Dot points of required input data and information

For example:

  • One or two examples of what is being tested in biological terms e.g. “What genes are differentially expressed in epithelial cells in Crohn’s disease vs healthy individuals?”

Steps:

  1. Breif description of steps involved in test
  2. If appropriate.

Worked example

Long example on real dataset.

Load Libraries and Data

…

Experimental Design

…

XXXX

…

Code Snippet

Copy and paste this bit into your own script to adapt to your own data. Make as generic as possible, just a framework.

# This code does not run

Results

# Display results table of stats

Have a dot point list of what every field in the default output is. Refer to docs wherever possible.

  • Column name 1 : This is xyz
  • Column name 2 : This is xyz

More information

List of useful resources. Papers, vignettes, pertinent forum posts

References

Phipson, Belinda, Choon Boon Sim, Enzo R Porrello, Alex W Hewitt, Joseph Powell, and Alicia Oshlack. 2022. “Propeller: Testing for Differences in Cell Type Proportions in Single Cell Data.” Bioinformatics 38 (20): 4720–26. https://doi.org/10.1093/bioinformatics/btac582. 

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8      compiler_4.3.2      BiocManager_1.30.22
 [4] renv_1.0.5          promises_1.2.1      Rcpp_1.0.12        
 [7] stringr_1.5.1       git2r_0.33.0        callr_3.7.6        
[10] later_1.3.2         jquerylib_0.1.4     yaml_2.3.8         
[13] fastmap_1.1.1       R6_2.5.1            knitr_1.45         
[16] tibble_3.2.1        rprojroot_2.0.4     bslib_0.7.0        
[19] pillar_1.9.0        rlang_1.1.3         utf8_1.2.4         
[22] cachem_1.0.8        stringi_1.8.3       httpuv_1.6.15      
[25] xfun_0.43           getPass_0.2-4       fs_1.6.3           
[28] sass_0.4.9          cli_3.6.2           magrittr_2.0.3     
[31] ps_1.7.6            digest_0.6.35       processx_3.8.4     
[34] rstudioapi_0.16.0   lifecycle_1.0.4     vctrs_0.6.5        
[37] evaluate_0.23       glue_1.7.0          whisker_0.4.1      
[40] fansi_1.0.6         rmarkdown_2.26      httr_1.4.7         
[43] tools_4.3.2         pkgconfig_2.0.3     htmltools_0.5.8.1