U-BDS offers bi to tri-annual workshops which cover the fundamentals of programming (R, Python, Unix, git). This material is taught by our very own Software Carpentry certified instructors (across the U-BDS team and the Center for Computational Genomics and Data Science team), with the aid of other members across both groups. To learn more about the Software Carpentry please visit: https://software-carpentry.org/
Our Bulk RNA-seq workshop materials can be found here.
This workshop covers the foundational topics and methods to bulk RNA-seq analysis, including:
nf-core/rnaseqDESeq2, gene
annotation, gene enrichment analysis (gene-ontology and gene set
enrichment analysis)While we will continue to offer programming workshops, we are also in
the planning phases of data analysis workshops. If interested, please
join the UAB Labs #datascience channel for upcoming
workshop announcements.
A summary of resources available to the UAB community (both open source solutions and service-based) have been compiled and presented at the UAB 2023 10X Genomics User Day by Dr. Lara Ianov. The slides are publicly available at here. We note that Seurat 5 has now been released in CRAN and is recommended for spatial analysis.
The nf-core community offers annual training covering various topics which are relevant to the community (from Nextflow, to nf-core pipelines, among others.). To learn more, please visit: https://nf-co.re/events/training. In addition to their formal training, they also host short talks named “Bytesize Talks” which cover a series of topics (e.g.: pipeline specific talks, to pipeline development areas etc.) - see more at https://nf-co.re/events/bytesize
UAB’s Research Computing (RC) provides a wealth of resources, available to all in the UAB community (e.g.: data transferring tools, High Performance Computing, their own office hours etc.). To learn more, please visit: https://docs.rc.uab.edu/.
Students who are seeking community involvement with other trainees are encouraged to reach out to the UAB Informatics Club: https://informaticsclub.github.io/. The Informatics club provides opportunities for students to practice their talks, troubleshoot their code and watch seminars which the club organizes, along with many other activities.