Student-led bioinformatics tools and resources (find @ github here)
tools
- Dylan Beeber (2020) CrispRdesignR: a versatile guide RNA design package in R for CRISPR/Cas9 applications
- Dylan wrote the code and designed this R package + GUI to develop guide RNA design for non-model organisms
- https://github.com/dylanbeeber/crispRdesignR
student-made video tutorials and manuals on bioinformatics tools
Command-line tools
R
Web-based tools, GUIs, and Databases
- Biopython (Eliza Doering)
- BLAST from the Command Line (Steven Blair)
- DIAMOND and BLAST from the Command Line (Ria Lamba)
- Orthofinder (David Blumsack)
- SNP calling from the Command Line (Reid Wiggins)
R
- R Markdown - How to compile your code in RStudio (Kenny Le)
- Allele specific expression in R using AllelicImbalance (Nick Hebert)
- Visualizing Genetic Variants in R using ggbio (Sam DeLap)
Web-based tools, GUIs, and Databases
- 3D Protein Modeling (Colin King)
- A Guide to Performing Differential Expression Analysis Using Galaxy Tools (Karina Calderon)
- Determining Potential Epitopes for Vaccine Candidacy Using IEDB - the Immune Epitope Database (Marcel Adamczyk)
- Exploring The Cancer Genome Atlas (John Loreti)
- IGV - Integrative Genomics Viewer (Preet Gami)
- KEGG pathway (Sarah Carnes)