Related Experiment Video
Updated: Feb 9, 2026
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones
Sören Müller1, Ara Cho1, Siyuan J Liu1
1Department 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.
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