/single_cell_RNAseq

Single cell RNA seq alignment and downstream processing

Primary LanguageR

single_cell_RNAseq

Single cell RNA seq alignment and downstream processing

Type of data: Drop-seq

Tools used for alignment: Salmon and Alevin

https://salmon.readthedocs.io/en/latest/alevin.html

https://combine-lab.github.io/alevin-tutorial/2018/running-alevin/

R Package used for single cell downstream analysis: Seurat

Note: Tutorial for integration of multiple datasets belonging to different experiments/replicates

https://satijalab.org/seurat/v3.0/immune_alignment.html

Note: Tutorial for a single experiment

https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html

R Package used for single cell trajectory analysis: Monocle

http://cole-trapnell-lab.github.io/monocle-release/docs/#constructing-single-cell-trajectories