Analysis of single cell RNA sequencing data.

This project uses the Seurat package to establish a workflow for the analysis of single cell RNA sequencing data. The used dataset is publicly available.

• Tissue: Retina of seven P14 mice
• Single Cell method: DropSeq

Original data from Macosko et. al.

available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63472

Reference:

Macosko EZ, Basu A, Satija R, Nemesh J et al. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 2015 May 21;161(5):1202-1214. PMID: 26000488

Necessary packages

• Seurat

optional:

• Rtsne openmp branch for parallel TSNE computation - https://github.com/jkrijthe/Rtsne
• umap-learn package for python - https://umap-learn.readthedocs.io/en/latest/