For better experience, turn on JavaScript!


SCmut

SCmut

SCmut is a tool for the detection of cells that contain mutations in RNA-seq and bulk-cell DNA-sequencing data. The SCmut algorithm can use a list of somatic mutations in the absence of DNA-sequencing data.

Topic

Genomics; Oncology; RNA-seq

Details

  • Operation: RNA-Seq analysis; Genetic variation analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: The Swedish Cancer Fonden, the Swedish Research Council (VR), the Swedish Foundation for Strategic Research (SSF).
  • Contact: Yudi Pawitan yudi.pawitan _at_ ki.se
  • Collection: -

Publications

Vu TN, Nguyen HN, Calza S, Kalari KR, Wang L, Pawitan Y "Cell-level somatic mutation detection from single-cell RNA-sequencing." Bioinformatics. 2019 Apr 26. pii: 5480302. https://doi.org/10.1093/bioinformatics/btz288
PMID: 31028395


Chung W, Eum HH, Lee HO, Lee KM, Lee HB, Kim KT, Ryu HS, Kim S, Lee JE, Park YH, Kan Z, Han W, Park WY "Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer." Nat Commun. 2017 May 5;8:15081. https://doi.org/10.1038/ncomms15081
PMID: 28474673
PMCID: PMC5424158


Download and documentation








If you find errors, please report here.