Frequently Asked Questions
This is the FAQ for the Bioconductor Support Site. Please visit
Bioconductor.org for additional project and package information. A list of
current Bioconductor packages can be found here
What is the difference between the support site and the bioc-devel mailing list?
Do not post to both locations! The support site is for questions related to
usage of Bioconductor packages and troubleshooting; This site is appropriate
for most questions. For guidance on developing a Bioconductor package,
including current and future implementation of functions and features, please
use the bioc-devel mailing list
What questions should I post?
The support site is for questions related to usage of Bioconductor packages.
Bioconductor package maintainers are required upon submission to subscribe
to the support site and are expected to answer questions regarding their
packages at this location. General questions about bioinformatics,
computational genomics, biological data analysis and software unrelated to
Bioconductor can be asked on biostars or
seqanswers. General R questions can be asked on the
R-help mailing list or
How do I contact you?
Those of us who maintain this site read the posts that are made here. So users
who wish to contact us are encouraged to post to this site.
What if I find a bug with the support site?
No site is perfect and you may come across things that you feel are not
working as they should be. This site is based on a fork of Biostars so we have
the power to correct many problems as they are discovered. If you find a
problem with this website, we ask that you please post such questions to our
Where can I suggest new features to the support site?
New feature requests can be made by opening an issue on the github
What about offensive content?
The Bioconductor project-wide code of conduct
upholds community values that all participants are expected to support.
TL;DR very abbreviated version: do not engage in online behavior contrary to
- diversity and inclusivity
- kindness and a welcoming environment
- openness in regard to software implementations
Users posting content that does not belong to the site will be notified and
required to edit their content. Users may post job postings to the 'Jobs' section as
long as the topic aligns with the main focus of this site. Users posting obvious spam
will be immediately suspended or banned. Moderators will try to remove offensive
content in a timely fashion but if you find something offensive please notify firstname.lastname@example.org.
Post not relating to Bioconductor content will generally be removed by moderators.
You can also make an anonymous or non-anonymous report via the following link: https://tinyurl.com/bioccomplaint.
It is a free-form text box that will be forwarded to the Code of Conduct Committee.
Alternatively you can email the Code of Conduct Committee (email@example.com).
If you are uncomfortable reporting to the Code of Conduct committee as a group, you can contact
any individual committee member via email or a direct message on the community-bioc Slack channel.
How do I write good posts?
One of the biggest things that new users struggle with is how to ask questions
in a way that allows people to answer them. So if you are unfamiliar please
have a look at the posting
guide for some great
advice and the tutorial for help
on using the markdown editor. If a Bioconductor package reports an error that
you cannot debug and are requesting assistance, Please check and include the
BiocManager::valid() reports your packages are of the correct version.
- Record the output of
traceback() immediately after the error occurs.
- Include the output of
- Provide minimal code necessary to try and reproduce the issue. StackOverflow has suggestions for making a reproducible example.
Please make also sure to phrase your questions, answers and comments in a welcoming,
supportive, collegial, and harassment-free way, in line with the
Bioconductor project-wide code of conduct.
How do I format a post?
The support site usese a markdown editor. There is a useful tutorial post with
additional helpful links found here.
How do I put images into my posts?
You can also put images and plots into your posts. All you need to do is
create (or login to) a free account with http://imgur.com and upload any
images or plots that you want to share. Then you can enter the imgur generated
'Direct Link' url into the 'URL' location that is available when you click on
the 'image' button in the text editor. The plot will be imbedded right into
What post tags are automatically suggested?
When creating a post, a user is required to enter at least one 'Post Tag'.
There will be automatically suggested tags. These tags are generated from the
current list of Bioconductor packages as well as biocViews.
How can I keep track of topics that interest me?
This site offers two ways to track posts when they use certain tags. You can
add the tags that you want tracked into your user profile. 'My Tags' will put
posts that match your tagging criteria into a special tab that you can check
whenever you log in. And 'Watched Tags' should actually email you whenever
someone posts using a tag that you are interested in.
What are the different post types?
When ASK A QUESTION is selected there are four options. Most often a user
should keep the "Ask a question" as the selected 'Post Type'. The four options
- Ask a question: For general questions and help
- Post a Job Opening: For recruiting new hires by posting open job opportunities for a related field appropriate to the Bioconductor community
- Share a Tutorial: Share a tutorial for a bioinformatic analysis or Bioconductor package
- Announce News: Announce breaking news about Bioconductor or package to the community at large
How do I post a Job, Tutorial, or News item?
Follow the ASK A QUESTION link and choose the appropriate field in the 'Post
Type' drop down box.
How do I filter posts?
There are a number of different ways to filter posts. A user can edit their
'My Tags' in their profile to allow specific posts in the 'My Tags' section of
the banner. To filter the main posting list, a user could search for a
specific term in the search field above the post listings. A user could also
filter using the 'Limit' and 'Sort' drop down boxes above the post listings.
How do I merge multiple previous acccounts?
So perhaps you have been using the Bioconductor mailing list for a long time
and during that time you have been using multiple different aliases. And now
you would like to consolidate things so that you can get credit for actually
being only one person. What should you do? Well 1st of all you should get set
up with the account that you normally use. If you have not logged in before
this may mean going straight to password recovery.
Once you can log in, you will want to click on your name and then go to the
little blue button that is called 'Social Login'. Here you should be able to
link in other social accounts that you may have used before (such as gmail) to
your primary account email.
If it turns out that your previous aliases are not listed as optional social
logins (as may happen if they were associated with different academic
institutions) then you will need to email us at firstname.lastname@example.org and
send us a file. This file needs to contain a single line that looks like this:
email1 email2 email3 etc. Essentially, this file should contain one email for
each account you wish to merge (separated by whitespace). And the very first
email that it lists must be the one that you want to regularly use as your
primary account for this site.
The number next to a user's name is the sum of upvotes and accepted answers
that user has collected. Upvotes boost your reputation on the site.
How do I edit my profile?
Navigate to your user account by either clicking on your name or go to the
list of users, search for your user name, and click on it. From this page, you
should be able to select 'Edit profile' under your gravatar/profile picture.
How do I update my profile picture?
What is a handle and how do I update it?
A handle is a convenient way for other users to tag you in a post so you
receive a email notification regarding the posting. If a users handle was
'user1', anyone could tag the user in a post with '@user1'. This triggers an
email notification for the post. A user can change their handle by editing
their profile. See previous section on editing profile.
What are the different notification options?
When editing your profile there are different notification options to choose
from. The following describe the options:
- Local Messages:
- No Messages:
What is the different between 'My Tags' and 'Watched Tags'?
'My Tags' controls which posts can be seen in the 'My Tags' tab. Any post with
the tags listed will show up in the tab. 'Watched Tags' controls email
postings. Any post with these tags will trigger an email notification about
the post. It is expected that package maintainers have their package selected
for at minimum 'Watched Tags'.
Does selecting a digest option change my notification option?
How are awards generated?
Awards are triggered automatically by performing actions or reaching
milestones required for the award.
What awards are available to earn?
Becoming a moderator
Moderators are selected by Bioconductor core team members. The
responsibility of moderating posts is given to long-term trusted users.
What shows up in 'Messages'?
The Messages tab shows awards earned and comments on posts.
What shows up in 'Votes'?
The Votes tab shows posts that have received an upvote, accepted answer, or if
someone has bookmarked your post.
What shows up in 'My Posts'
Any post that you have created, answered or commented appear in this tab.
What shows up in 'My Tags'
Any post with the tags identified in 'My Tags' of a user's profile are listed
under this tab. These can be edited by updating/editing your user profile.
What shows up in 'Follow'?
What shows up in 'Bookmarks'? / How do I bookmark a post?
After selecting a post, there is a bookmark icon underneath the upvote count
for the main post, as well as any answer, comment, or reply.
What does selecting a digest option do? Does it effect my notification option?
What HTML tags allowed in the post content
Can't find what your looking for? Consider opening an issue on the
support.bioconductor.org github issues.