Tools

This page lists the computational tools developed by the CIT team for genomic data analysis.

  • FounderTracker is an R program for detecting significantly recurrent identity by descent (IBD) in a set of haplotypes (Letouzé et al., PLoS ONE 2012).
  • citbcmst is an R package to predict the breast cancer molecular subtypes from Guedj et al. (Oncogene 2012).
  • citccmst  is an R package to predict the 6 molecular subtypes of colon cancer described in Marisa et al. (PLoS Medicine 2013).
  • citBladderCancerBLMST is an R package to predict the membership of an expression profil to the bladder cancer Basal-Like Muscle-invasive SubType, as described in Rebouissou et al. (Science Translational Medicine 2014)
  • Annotator is the CIT program information system (private and secure access only).
  • MCP-counter is an R package which predicts the abundance of 10 cell populations (8 immune populations, endothelial cells and fibroblasts) from transcriptomic profiles of human tissues.