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SCLab

SCLab is an interactive single-cell RNA-seq analysis toolkit for Jupyter notebooks. It wraps AnnData and Scanpy with a reactive, widget-based dashboard so you can explore, preprocess, cluster, and visualize your data without leaving your notebook.

Features

  • Interactive dashboard — tabbed layout with a live scatter plot, interactive tables, and a step-by-step analysis panel
  • Standard scRNA-seq workflow — QC, normalization, PCA, batch integration, neighbors, UMAP, clustering, all in one place
  • Doublet detection — Scrublet, DoubletDetection, scDblFinder
  • Differential expression — pseudobulk analysis with edgeR or limma (optional R integration)
  • Pseudotime & trajectory analysis — draw a path on the UMAP and let SCLab compute pseudotime
  • Extensible — add custom analysis steps with a simple subclass API

Quick Start

import scanpy as sc
from sclab import SCLabDashboard

adata = sc.read_10x_h5("data.h5")
dashboard = SCLabDashboard(adata, name="My Analysis")
display(dashboard)

Then run the built-in steps in sequence from the sidebar panel:

  1. QC — filter cells and genes, inspect barcode rank plot
  2. Preprocess — normalize, log-transform, scale
  3. PCA — dimensionality reduction
  4. Neighbors — build the k-NN graph
  5. UMAP — 2D/3D embedding
  6. Cluster — Leiden clustering

Installation

pip install sclab

See the Installation guide for full details including optional dependencies.