3 How to ask for help

In general we prefer that you contact us through a public forum such that others can benefit from your answers, so please avoid emails as much as possible. Leonardo has written a more extensive page on how to ask for help in general beyond this project which might be useful for you. While we have multiple options for you to contact us, please avoid posting your question in all the forums.

3.1 Gitter

We have several Gitter chats setup in relation to our software. Here’s some of them:

• Megadepth: https://gitter.im/megadepth/community
• Snaptron: https://gitter.im/snaptron/Lobby

3.2 Bioconductor Support website

For our R/Bioconductor packages, you can ask for help through the Bioconductor support website using the appropriate tags:

• recount3: https://support.bioconductor.org/tag/recount3/
• snapcount: https://support.bioconductor.org/tag/snapcount/
• megadepth: https://support.bioconductor.org/tag/megadepth/

3.3 GitHub Issues

You can also report bugs through GitHub issues. Ideally, use the repository that contains the code that has produced the bug. For example, for the recount3 R/Bioconductor package use https://github.com/LieberInstitute/recount3/issues.

Here’s a list of possible locations:

R/Bioconductor related:

• recount3: https://github.com/LieberInstitute/recount3/issues
• megadepth: https://github.com/LieberInstitute/megadepth/issues
• snapcount: https://github.com/langmead-lab/snapcount/issues

Tools:

• Megadepth: https://github.com/ChristopherWilks/megadepth/issues
• Snaptron: https://github.com/ChristopherWilks/snaptron/issues

Monorail system related:

• monorail-external: https://github.com/langmead-lab/monorail-external/issues
• recount-pump: https://github.com/langmead-lab/recount-pump/issues
• recount-unify: https://github.com/langmead-lab/recount-unify/issues

Documentation related:

• recount3-docs: https://github.com/LieberInstitute/recount3-docs/issues (where this website is created)