7 Related software

As part of recount3 we provide bigWig files for each sample. These files can be used to re-quantify the expression levels with new annotations using the same reference genomes. They can also be used to explore un-annotated regions of the genome. For recount3 we suggest using the megadepth R/Bioconductor package (or the command-line version) available from https://bioconductor.org/packages/megadepth.

Additionally, we have written quite a bit of code for recount3 that is is available through different GitHub repositories. You can find our main products at recount.bio ⁴. Some of our software related to recount3 are highlighted below.

R/Bioconductor related:

• recount3: https://github.com/LieberInstitute/recount3 or https://bioconductor.org/packages/recount3
• megadepth: https://github.com/LieberInstitute/megadepth or https://bioconductor.org/packages/megadepth
• snapcount: https://github.com/langmead-lab/snapcount or https://bioconductor.org/packages/snapcount

Tools:

• Megadepth: https://github.com/ChristopherWilks/megadepth also available from anaconda at https://anaconda.org/bioconda/megadepth
• Snaptron: https://github.com/ChristopherWilks/snaptron

Monorail system related:

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

Documentation related:

• recount3-docs: https://github.com/LieberInstitute/recount3-docs (where this website is created)
• duffel: https://github.com/nellore/duffel for providing permalinks

7.1 Beyond recount3

We have more software beyond recount3 including:

• recount: https://bioconductor.org/packages/recount (for accessing the recount2 data)
• ASCOT: http://ascot.cs.jhu.edu/
• recountmethylation: https://bioconductor.org/packages/recountmethylation
• Rail-RNA and Rail-dbGaP: http://rail.bio/
• derfinder: https://bioconductor.org/packages/derfinder
• recount.bwtool: https://github.com/LieberInstitute/recount.bwtool (now defunct given megadepth which is much faster, easy to install, and available through Bioconductor)

Documentation related:

• recount-website: https://github.com/leekgroup/recount-website for recount2
• recountWorkflow: https://bioconductor.org/packages/recountWorkflow and several workshops such as https://github.com/LieberInstitute/recountWorkshop2020
• recount-contributions: https://github.com/leekgroup/recount-contributions (now defunct given how you can use the Monorail system to process your data and share it with us)

Some other software we have written can be found at:

• https://github.com/ChristopherWilks?tab=repositories
• https://github.com/langmead-lab?tab=repositories
• https://github.com/LieberInstitute?tab=repositories
• https://github.com/kasperdanielhansen?tab=repositories
• https://github.com/nellore?tab=repositories
• https://github.com/leekgroup?tab=repositories
• https://github.com/lcolladotor?tab=repositories

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4. Test version is available at http://nellore.bio/recount-landing/.↩︎