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Resources

The Section of Developmental Biology makes use of various technologies to study embryonic development. This page contains links to tutorials and other resources for commonly used methods.

Single cell RNA-seq:

Integrated Development Environments

Jupyter Notebook:

RStudio:

Prep Samples for Analysis

Cell Ranger:

Seurat

Scanpy

Scanpy Tutorials:

Theis Lab Tutorial:

Trajectory/Pseudotime Analysis

Slingshot:

tradeSeq:

RNA Velocity:
https://scvelo.readthedocs.io/

Functional Enrichment Analysis

GoProfiler:

Best Practice Reviews

Theis Lab Best Practice Review: 

RNA Fish