Kleinman lab

braindex

braindex is a web portal for interrogating a single-cell RNAseq atlas of the developing mouse brain. We generated and described this dataset, which catalogs over 60,000 cells from the mouse forebrain and pons at several different timepoints, in our 2019 publication, Stalled developmental programs at the root of pediatric brain tumors. Check out the portal for several visualizations and tools for interrogating a gene or gene set of interest across cell types, brain regions, and developmental time.

cc-shiny-01.functionalgenomics.ca/braindex/clusters/
Check out the project on GitHub

scCoAnnotate

scCoAnnotate is a Snakemake pipeline for efficient reference-based consensus prediction of cell-types in single-cell RNA sequencing (scRNA-seq) data. This automated workflow allows users to run 15 different statistical and machine learning tools to predict cell type labels of scRNA-seq samples. It outputs a consensus of the predictions, which has been found to have increased accuracy in benchmarking experiments compared to the individual predictions alone.

Check out the project on GitHub