/single-cell-tools

Primary LanguageR

Utility Scripts

A collection of utility scripts to help with tasks related to scRNA.

  1. Pre/Post processing tasks.
  2. Visualization (Cellxgene)
  3. TBD

Installation

[Optional] Install a custom virtualenv for r-reticulate

By default, r-reticulate will create a python virtualenv at ~/.virtualenv/r-reticulate. Instead, we can create our own and manage our python dependencies separate from the default location.

python3 -m venv ./.venv
source ./.venv/bin/activate
pip install -r requirements.txt

Then in RScript

library("reticulate")
use_virtualenv("./.venv")
loompy <- reticulate::import("loompy")

Format Conversion

Seurat v5 installation

seuratv5 to anndata (h5ad)

Visualization

Cellxgene

cellxgene launch </path/to/myfile.h5ad>