A repository of standardized single cell RNA-Seq datasets for analysis and visualization at the single cell level
Choose text tutorial or video tutorial to learn to visualize downloaded data with IGV (Integrative Genomics Viewer).
If you find this resource useful, please mention this site (Ner-Gaon et al. 2017, JI).
Immune Related Datasets
Datasets which are not immune related
Update (11/11/24):
Due to the increased number of scRNA-seq, we no longer maintain JingleBells. However, cell specific tags are now associated with the reads in many scRNA-seq datasets, which makes our format redundant. You can open the FASTA/FASTQ file and see if any of the tags of the reads (appear in the title row of the read) exist. If so, you can color the reads by cell in IGV using the tag.
To do so, after you upload the bam file(s) into IGV:
1. Hover the mouse over the track name, right click the mouse, choose group by, choose tag, and type the tag name. The reads from each single cell will be grouped together.
2. Hover the mouse over the track name again, right click the mouse, choose color by, and choose the tag name. The reads from each single cell will be colored by the same color.
For inquiries, please write to talshay@bgu.ac.il.