Tutorial:Updated Support Site Editor
0
15
Entering edit mode
shepherl 4.1k
@lshep
Last seen 1 day ago
United States

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.

support.bioconductor.org editor markdown updates Tutorial • 9.8k views
ADD COMMENT
2
Entering edit mode

For those interested in video format, please see the links below to RMarkdown Coursera course sections:


Note. We are not affiliated, associated, authorized, endorsed by, or in any way officially connected with Coursera Inc., or any of its subsidiaries or its affiliates. The official Coursera website can be found at https://www.coursera.org/. The name “Coursera” as well as related names, marks, emblems and images are registered trademarks of Coursera Inc.

ADD REPLY
0
Entering edit mode

Hi. thank you. I can not submit my question. After clicking on the submit button, the color of the textbox dedicated for the question becomes red and I can't fix it. Apparently, the text of my question has not any problem. I do not know what I should do. Can you help me, please?

ADD REPLY
0
Entering edit mode

Have you added appropriate tags? You need to tag a Bioconductor package or "Bioconductor". Also there is a limitation on special characters. We check to make sure text is ASCII and it will not post if there are special characters present.

ADD REPLY
0
Entering edit mode

Thank you. The ASCII was the case. I used an online tool to find the non-ASCII chars and after deleting those chars, it was fixed. Thank you again.

ADD REPLY

Login before adding your answer.

Traffic: 417 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6