- To run many of these scripts, users must have access to a high performance computing environment. They are often in pairs with the same name, with the shell script (ex. shell.sh) created to submit the working script (shell.R) to an HPC environment.
- The user must update the bash script to the appropriate parameters for their unique HPC. These were built on an HPC using command line with SLURM.
| Pipeline | Description |
|---|---|
🧬 Bulk RNAseq |
Basic pipeline for bulk RNA-sequencing experiments from preprocessing to downstream pathway analysis |
📦 PackageBuilding |
Helper scripts for building an R package |
📊 Visualizations |
Basic visualization scripts for common plots such as volcano plots |
🎯 miRNA |
Scripts for analysis of miRNA |
🧬 scDNAseq/MissionBio Tapestri |
Analysis scripts for MissionBio Tapestri platform data using the optima package and hardcoding analysis |
🔍 scRNAseq |
Basic analysis for scRNAseq from 10X platforms |
🧭 spatial RNAseq/VisiumHD |
Scripts from analyses of Visium HD samples for preprocessing, quality control, integration using scVI, nucleus segmentation using stardist, differential expression analysis, cell type ID via RCTD |
✍️ Maintained by Rachel Griffard-Smith
📫 Contact: Leave a note in the Issues or Pull requests section