SoptSc: Cell lineage and communication network inference via optimization for single-cell transcriptomics.

What is being modeled?

Cellular trajectories, cell-cell communications

Description & purpose of resource

Implementation of pattern recognition algorithms and visualization tools for similarity and communication between cells and populations of cells.

Spatial scales

cellular

tissue

Temporal scales

1 - 103 s

hours

days

weeks to months

This resource is currently

mature and useful in ongoing research

Has this resource been validated?

Yes

Link to Resource Credibility Assessment

SoptSc: Cell lineage and communication network inference via optimization for single-cell transcriptomics

Can this resource be associated with other resources? (e.g.: modular models, linked tools and platforms)

Yes

Key publications (e.g. describing or using resource)

Shuxiong Wang, Matthew Karikomi, Adam L MacLean, Qing Nie. Cell lineage and communication network inference via optimization for single-cell transcriptomics. Nucleic Acids Research, Volume 47, Issue 11, 20 June 2019, Page e66. DOI: 10.1093/nar/gkz204.

DOI link to publication describing this resource

10.1093/nar/gkz204

Link to resource

RSoptSC (R)

SoptSC (Matlab)

Collaborators

Qing Nie

PI contact information

qnie@uci.edu