NanoStringNormCNV

About

Helper functions to pre-process and call CNVs on NanoString DNA data.

Dependencies

  • R (>= 3.0.2)
  • lattice (>= 0.20-27)
  • BoutrosLab.plotting.general (>= 3.6.20)
  • mclust (>= 4.4)
  • gdata (>= 2.8.2)
  • futile.logger (>= 1.3.7)
  • testthat
  • reshape2 (>= 1.4)
  • vsn (>= 3.22.0)
  • NanoStringNorm (>= 1.1.18)
  • vegan
  • googleVis (>= 0.2.14)

Installation

To install in an interactive R session, do the following:
install.packages("NanoStringNormCNV", repos = "http://bpg.oicr.on.ca")
This will install NanoStringNormCNV and it's dependencies from our miniCRAN repository.

Mac users will need to do the following before installing the package in R:
  • Ensure that your Xcode license is accepted with the following command:
    sudo xcodebuild --license
  • If fortran is not installed, install it with the following commands:
    curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
    sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
  • Set up your active developer directory for Xcode and BSD tools:
    xcode-select --install

API

A detailed description of all functions and their parameters can be found in the API.

Downloads

Version 1.1.1
2.8 MB
PDF Guide
1.12 MB