This repository has example notebooks that demonstrate usage of kallisto bus to generate gene count or (transcript compatibility count) TCC matrices from FASTQ files and some basic downstream analyses. To run the notebooks, please install kallisto, bustools, and the BUSpaRse R package.
- 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (10x v2 chemistry); demonstration of
bustools - 1k PBMCs from a Healthy Donor (10x v3 chemistry); demonstration of
TENxBUSDataandBUSpaRse - RNA velocity with 10k E18 mouse neurons from 10x (coming soon)
- Differential expression with equivalence classes in TCC matrix (coming soon)