The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Tutorial: Updated Support Site Editor
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gravatar for shepherl
22 days ago by
shepherl ♦♦ 1.1k
United States
shepherl ♦♦ 1.1k wrote:

You may have noticed in a recent round of updates to the support site, there is a new editor for posting. The default editor now uses markdown by default rather than being a plain text editor. You can still type as normal but there are some key features to be aware of with markdown. Some cheat sheets/help pages, at least that I have found helpful, can be found at

As this is an mardown plugin for the editor not all the markdown syntax is activated but the above references can serve as a general guideline. The editor will also support html tags for formatting if that is preferred.

If anyone else has other cheat sheets or help pages they recommend please feel free to post as additional comments.

The editor should display some helpful buttons for formatting code and offers a preview of what your posting will look like after rendering below the posting text box. We are working on making it automatic that the website resets to see the new editor properly, however if you continually do not see the new editor properly please try clearing your web browsers cache and browsing history.

Here are some brief markdown tips to get you started and make your post more readable:

To encapsulate code that you cut and paste from your R session please use a triple backtick (```). You do not need to specify a coding language for syntax highlighting it will do it automatically.
So for example:

I am writing a post and describing what my issues is. Now I want to include my code chunk and ERROR output from terminal. So I will copy the code from my R terminal, initiate a code chunk with a triple backtick (this is a verbatim environment), paste my code, and close with a triple backtick. 

```
# I will copy code from terminal here

> library(BiocFileCache)
Loading required package: dbplyr

> library(PackageNotFound)
Error in library(PackageNotFound) : 
  there is no package called 'PackageNotFound'

> sessionInfo()
R Under development (unstable) (2019-01-29 r76024)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/lori/bin/R-devel/lib/libRblas.so
LAPACK: /home/lori/bin/R-devel/lib/libRlapack.so

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] BiocFileCache_1.7.0 dbplyr_1.3.0        BiocManager_1.30.4 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       bindr_0.1.1      magrittr_1.5     rappdirs_0.3.1  
 [5] tidyselect_0.2.5 bit_1.1-14       R6_2.3.0         rlang_0.3.1     
 [9] blob_1.1.1       httr_1.4.0       dplyr_0.7.8      tools_3.6.0     
[13] DBI_1.0.0        bit64_0.9-7      assertthat_0.2.0 digest_0.6.18   
[17] tibble_2.0.1     crayon_1.3.4     bindrcpp_0.2.2   purrr_0.2.5     
[21] curl_3.3         memoise_1.1.0    glue_1.3.0       RSQLite_2.1.1   
[25] compiler_3.6.0   pillar_1.3.1     pkgconfig_2.0.2 

```

It will display like so:

# I will copy code from terminal here

> library(BiocFileCache)
Loading required package: dbplyr

> library(PackageNotFound)
Error in library(PackageNotFound) : 
  there is no package called 'PackageNotFound'

> sessionInfo()
R Under development (unstable) (2019-01-29 r76024)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/lori/bin/R-devel/lib/libRblas.so
LAPACK: /home/lori/bin/R-devel/lib/libRlapack.so

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] BiocFileCache_1.7.0 dbplyr_1.3.0        BiocManager_1.30.4 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       bindr_0.1.1      magrittr_1.5     rappdirs_0.3.1  
 [5] tidyselect_0.2.5 bit_1.1-14       R6_2.3.0         rlang_0.3.1     
 [9] blob_1.1.1       httr_1.4.0       dplyr_0.7.8      tools_3.6.0     
[13] DBI_1.0.0        bit64_0.9-7      assertthat_0.2.0 digest_0.6.18   
[17] tibble_2.0.1     crayon_1.3.4     bindrcpp_0.2.2   purrr_0.2.5     
[21] curl_3.3         memoise_1.1.0    glue_1.3.0       RSQLite_2.1.1   
[25] compiler_3.6.0   pillar_1.3.1     pkgconfig_2.0.2 

If it is a short piece of code you wish to distinguish in-line you can use a single backtick (`) So `library(BiocManager)` would display as library(BiocManager)

While there should be bold and italics buttons on the editor there is shorthand syntax that can also be used; bold can be indicated with a double star ** or double underscore __and italic with single star * . Html tagging can also be used <b> and <em>

So

This will be **bold** and so will this __bold__

This will be *italic*

This will be <b> bold </b> and this will be <em> italic </em>

Will display as :

This will be bold and so will this bold

This will be italics

This will be bold and this will be italics



Please see the other links above on more markdown syntax.

ADD COMMENTlink written 22 days ago by shepherl ♦♦ 1.1k
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