Visualization of gene expression data from GeoMx-DSP experiments
Welcome everyone! This is the GEVisor 2021 Moffitt Hackathon GitHub page.
If it is of interest to utilize R for parts of this project (mostly for the Shiny side of things), it is recommended to download the appropriate version of R for your operating system from CRAN. Additionally, a great GUI for R is RStudio which can be downloaded here. Both of this make a powerful environment for working on projects.
Some useful packages that we can leverage when workin within R are:
- edgeR
- xCell
- limma
- spatialGE
- Seurat
- tidyverse
If you are versed in downloading packages from repositories other than CRAN, feel free to install spatialGE (devtools::install_github()) and edgeR, xCell, and limma (BiocManager::install()), otherwise we can install them tomorrow.
In addition to previously mentioned packages, we may explore implementation of the SpaGCN algorithm (Python) to detect differentially expressed genes.
GeoMx Data Downloads:
For some reading about analyzing the spatial data GeoMx, here is a link to the vignette for GeoMx analysis using spatialGE