Downloaded over 20,000 times and cited in over 400 peer-reviewed publications. AltAnalyze has hundreds of active users and is being actively developed as an open-source project.

AltAnalyze recieves funding from NIH National Cancer Institute (R01CA226802).


: See our new manuscripts describing the AltAnalyze workflows ICGS2 and cellHarmony and their application, in new article in Nature.




Cell-level matching and comparison of single-cell transcriptomes

cellHarmony is a cell-matching algorithm designed to identify a cell's most similar analogue in a distinct single-cell RNA-Seq (scRNA-Seq) dataset and find differentially expressed genes in each cell population. A manuscript describing cellHarmony can be found here. A set of data for analysis can be found in the latest version of AltAnalyze in the DemoData/cellHarmony folder along with instructions.