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.
- Help for clearing cache and history
- Clearing cache chrome
- Clearing firefox cache
- Clearing cache Internet Explorer
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.
For those interested in video format, please see the links below to RMarkdown Coursera course sections:
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?
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.
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.