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bigSCale

bigSCale

A framework tool to analyze and visualize single-cell RNA-seq data. The bigSCale functions support clustering, differential expression analysis, phenotype, pseudo-time analysis, inference of gene regulatory networks (GRNs), dataset minimizing. The algorithm estimates models using large sample sizes using a directed convolution strategy to estimate models and cope with noise. Alternative name: bigSCale2

Topic

Gene expression; RNA-seq

Details

  • Operation: RNA-Seq analysis
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: v1.7
  • Maturity: Stable
  • Credit: the Spanish Institute of Health Carlos III (ISCIII), Fundación Ramón Areces, the marathon “Todos Somos Raros, Todos Somos Únicos”, Marie Skłodowska-Curie Actions fellowship, Generalitat de Catalunya.
  • Contact: Holger Heyn holger.heyn _at_ cnag.crg.eu
  • Collection: -

Publications

Iacono Giovanni, Mereu Elisabetta, Guillaumet-Adkins Amy, Corominas Roser, Cuscó Ivon, Rodríguez-Esteban Gustavo, Gut Marta, Pérez-Jurado Luis Alberto, Gut Ivo, Heyn Holger "bigSCale: an analytical framework for big-scale single-cell data" bioRxiv https://doi.org/10.1101/gr.230771.117


Iacono G, Massoni-Badosa R, Heyn H "Single-cell transcriptomics unveils gene regulatory network plasticity." Genome Biol. 2019 Jun 4;20(1):110. https://doi.org/10.1186/s13059-019-1713-4
PMID: 31159854
PMCID: PMC6547541


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