Name
Title | ||
|---|---|---|
CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones. |
Abstract | ||
|---|---|---|
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. Contact: aaron.diaz@.ucsf.edu Supplementary information: Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2018 | 10.1093/bioinformatics/bty316 | BIOINFORMATICS |
Field | DocType | Volume |
Computer science,Gene expression,DNA sequencing,Computational biology,Bioinformatics | Journal | 34 |
Issue | ISSN | Citations |
18 | 1367-4803 | 0 |
PageRank | References | Authors |
0.34 | 1 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Sören Müller | 1 | 0 | 0.34 |
| Ara Cho | 2 | 0 | 0.34 |
| Siyuan J. Liu | 3 | 0 | 0.34 |
| Daniel A. Lim | 4 | 7 | 1.30 |
| Aaron Diaz | 5 | 7 | 1.64 |