Analysis Extentions

What else is out there in the scRNAseq analysis

• We have been looking mostly to what’s available within the R-language in general, and Seurat in particular. That means we skipped the Python’s alternative for SC analysis, Scanpy; and its underlying data structure (AnnData.) Together with their variational inference framework.

There are many other tools, it’s good you keep them in your radar in case the need arises…

• Spatial RNAseq analysis (Seurat) -> https://satijalab.org/seurat/articles/spatial_vignette.html

• Integration of scRNAseq and ATACseq data (Seurat) -> https://satijalab.org/seurat/articles/atacseq_integration_vignette.html

• sc-verse: python packages for scRNA/chromatin or spatial seq -> https://scverse.org/

• Monocle3: trajectory analysis -> https://cole-trapnell-lab.github.io/monocle3/docs/trajectories/

• RNA velocity analysis -> http://velocyto.org/, https://scvelo.readthedocs.io/en/stable/ (python)

• Also, worth to take a look at the Bioconductor set of packages for SC Analysis.

• Tidyomics, is a new ecosystem bringing SingleCellExperiment and SeuratObject to the tidyverse idioms. Have a look at their manifesto for a brief overview, and a neat presentation.