CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones.
Sören Müller, Ara Cho, Siyuan J Liu, Daniel A Lim, Aaron Diaz
Author Information
Sören Müller: Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
Ara Cho: Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
Siyuan J Liu: Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
Daniel A Lim: Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
Aaron Diaz: Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
Motivation: Single-cell RNA-sequencing (scRNA-seq) has enabled studies of tissue composition at unprecedented resolution. However, the application of scRNA-seq to clinical cancer samples has been limited, partly due to a lack of scRNA-seq algorithms that integrate genomic mutation data. Results: To address this, we present. CONICS: COpy-Number analysis In single-Cell RNA-Sequencing. CONICS is a software tool for mapping gene expression from scRNA-seq to tumor clones and phylogenies, with routines enabling: the quantitation of copy-number alterations in scRNA-seq, robust separation of neoplastic cells from tumor-infiltrating stroma, inter-clone differential-expression analysis and intra-clone co-expression analysis. Availability and implementation: CONICS is written in Python and R, and is available from https://github.com/diazlab/CONICS. Supplementary information: Supplementary data are available at Bioinformatics online.
