This repository contains prebuilt Pixi workspaces for common genomic and single-cell analysis workflows. Each workspace includes a pixi.toml and pixi.lock file to enable reproducible installation of R, Python, and Bioconductor packages across platforms. These environments are intended to make it easier to launch analyses without manually resolving package versions or dependencies.
Purpose: Skeleton environment for single-cell RNA-Sequencing analysis using Seurat v5.
Description:
- Includes all major R packages for single-cell workflows:
Seurat(v5.4+)SeuratObject- Bioconductor packages:
scater,scran,SingleCellExperiment,scDblFinder - Visualization:
ggplot2,patchwork,ggalluvial,viridis,RColorBrewer,ggrepel - Data manipulation:
dplyr,reshape2,Matrix - Monocle3: Trajectory inference for single-cell RNA-seq
- scplotter: Visualization utilities for single-cell data
Downstream analysis of bulk ATAC-Seq data in R and DeepTools (currently only for hg38)