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:
https://jupyter.org/
RStudio:
https://rstudio.com/products/rstudio/
Prep Samples for Analysis
Cell Ranger:
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Seurat
https://satijalab.org/seurat/vignettes.html
https://github.com/quadbiolab/scRNAseq_analysis_vignette/blob/master/Tutorial.pdf
Scanpy
Scanpy Tutorials:
https://scanpy.readthedocs.io/en/stable/tutorials.html
Theis Lab Tutorial:
https://github.com/theislab/single-cell-tutorial/blob/master/latest_notebook/Case-study_Mouse-intestinal-epithelium_1906.ipynb
Trajectory/Pseudotime Analysis
Slingshot:
https://github.com/kstreet13/slingshot
tradeSeq:
https://statomics.github.io/
RNA Velocity:
https://velocyto.org/
https://scvelo.readthedocs.io/
Functional Enrichment Analysis
GoProfiler:
https://biit.cs.ut.ee/gprofiler/gost
Best Practice Reviews
Theis Lab Best Practice Review:
https://www.embopress.org/doi/full/10.15252/msb.20188746