lutrarutra/scout

Tools for Single-Cell mRNA-seq (sc RNA-seq) Analysis

scout - reproducible single-cell data analysis with interactive visualisations.

scRNA-data is handled with ScanPy, plots made with Plotly.

Pipeline: Colab

Quality Control Violins

Mitochondrial Scatter Plot

Dispersion Plot

PCA Projection

PCA Correlation Circle

PCA Explained Correlation (w.r.t. categorical variables)

PCA Explained Variance

UMAP Projection

Trimap Projection

3D Projection (Looks better live)

DE Volcano

Heatmap

GSEA Volcano

Additional plots for Matplotlib (old stuff)

Volcano Plot

P-value & Marker Score Distributions

Marker Score

Clustered Heatmap i.e. Clustermap

GSEA Volcano

Sorted Heatmap

How to use?

1. conda env create -f environment.yml
2. conda activate scout
3. pip install -e .
4. import scout