ReNE 1.95 – A Cytoscape Plugin for Regulatory Network Enhancement

ReNE 1.95

:: DESCRIPTION

ReNE plugin, is a new Cytoscape 3.x plugin, which enables integration, merging, enhancement, visualization, and exporting of pathways from multiple repositories.

::DEVELOPER

The SysBIO research group

:: SCREENSHOTS

ReNE

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE
  • Cytoscape

:: DOWNLOAD

 ReNE

:: MORE INFORMATION

Citation

PLoS One. 2014 Dec 26;9(12):e115585. doi: 10.1371/journal.pone.0115585. eCollection 2014.
ReNE: a cytoscape plugin for regulatory network enhancement.
Politano G, Benso A, Savino A, Di Carlo S.

SCATE – Single-cell ATAC-seq Signal Extraction and Enhancement

SCATE

:: DESCRIPTION

SCATE integrates information from co-activated CREs, similar cells, and publicly available regulome data to substantially increase the accuracy for estimating individual CRE activities in single cell and rare cell subpopulations.

::DEVELOPER

Zhicheng Ji

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

SCATE

:: MORE INFORMATION

Citation

Ji Z, Zhou W, Hou W, Ji H.
Single-cell ATAC-seq signal extraction and enhancement with SCATE.
Genome Biol. 2020 Jul 3;21(1):161. doi: 10.1186/s13059-020-02075-3. PMID: 32620137; PMCID: PMC7333383.

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