title: RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy.
abstract: Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex. RAPIDR has been extensively tested with a large sample set as part of the RAPID project in the UK. The package contains quality control steps to make it robust for use in the clinical setting.
  
  
  METHODS
  RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html.
  
  
  BACKGROUND
  kitty.lo@ucl.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: University College London Genetics Institute, University College London, UK and North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK.
authors.forename: Kitty K
authors.initials: KK
authors.lastname: Lo
authors.affiliation: University College London Genetics Institute, University College London, UK and North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK.
authors.forename: Christopher
authors.initials: C
authors.lastname: Boustred
authors.affiliation: University College London Genetics Institute, University College London, UK and North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK.
authors.forename: Lyn S
authors.initials: LS
authors.lastname: Chitty
authors.affiliation: University College London Genetics Institute, University College London, UK and North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK.
authors.forename: Vincent
authors.initials: V
authors.lastname: Plagnol
mesh_terms: D000782:Aneuploidy; D016477:Artifacts; D019295:Computational Biology / Q000379:methods*; D005260:Female; D006801:Humans; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D012737:Sex Factors; D012984:Software; D014314:Trisomy / Q000175:diagnosis / Q000235:genetics; D014424:Turner Syndrome / Q000175:diagnosis / Q000235:genetics