SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
Develop a long format workshop to teach in 1 day (could be up to 2 days) the basics of bulk RNA-seq data and alignment. This would build upon previous SPEAQeasy-based Bioconductor workshops that are at most 90 min long. Those are not long enough to learn how to install SPEAQeasy, download a small example dataset such as the one we have at https://research.libd.org/SPEAQeasy-example/prepare_data.html, run SPEAQeasy, and then inspect the results.
We might want to learn about the format used by https://carpentries.org/index.html for short courses prior to designing this short course / long workshop. The target audience would be users who have some basic familiarity with bulk RNA-seq data.
Similar to https://github.com/LieberInstitute/spatialLIBD/issues/68
Develop a long format workshop to teach in 1 day (could be up to 2 days) the basics of bulk RNA-seq data and alignment. This would build upon previous
SPEAQeasy-based Bioconductor workshops that are at most 90 min long. Those are not long enough to learn how to installSPEAQeasy, download a small example dataset such as the one we have at https://research.libd.org/SPEAQeasy-example/prepare_data.html, runSPEAQeasy, and then inspect the results.We might want to learn about the format used by https://carpentries.org/index.html for short courses prior to designing this short course / long workshop. The target audience would be users who have some basic familiarity with bulk RNA-seq data.