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

General

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 StackOverflow.

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 github repository.

Where can I suggest new features to the support site?

New feature requests can be made by opening an issue on the github repository.

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 webmaster@bioconductor.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 (code-of-conduct@bioconductor.org). 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.

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Posts

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 following:

  • That BiocManager::valid() reports your packages are of the correct version.
  • Record the output of traceback() immediately after the error occurs.
  • Include the output of sessionInfo().
  • 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 your post.

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 are:

  • 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.

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Account

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.

After setting up the primary account, that contact the site admins to resolve the issue.

User reputation

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:

  • Default:
  • Email:
  • 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.

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Banner

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?

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What HTML tags allowed in the post content

Font styling:

  • b, i,img, strong, strike, em, underline
  • sub, sup, img
  • h1 , h2, h3, h4

Content layouts:

  • div, span, br,p, hr

Code render

  • code, pre

Tables -table, thead, tr, th, td, tbody

Allowed styles:

  • color
  • font-weight
  • background-color
  • width height

Other

Can't find what your looking for? Consider opening an issue on the support.bioconductor.org github issues.

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