A pipeline for the meta-analysis of gene expression data. We have assembled several analysis and plot functions to perform integrated multi-cohort analysis of gene expression data (meta- analysis). Methodology described in: < http://biorxiv.org/content/early/2016/08/25/071514>.
This is README space for metaIntegrator_public. To be filled with a README if necessary, or for internal use if required.
For the current version on CRAN:
For the current development version:
Run the following lines in R:
install_bitbucket("khatrilab/metaIntegrator_public", auth_user=USERNAME, password=PASSWORD)
where USERNAME and PASSWORD are your bitbucket username and password.
If you get "ERROR: dependency ‘deapathways’ is not available for package ‘MetaIntegrator’", follow these steps:
deapathways_1.0.tar.gz file (which is stored in metaIntegrator_public/inst).
install deapathways, either by going to the command line, navigating to the folder containing
tar.gz file in the command line and running
R CMD INSTALL deapathways_1.0.tar.gz,
or by running
install.packages(PATH_TO_FILE, repos = NULL, type="source")
PATH_TO_FILE is the path to the
To read the Vignette go to: http://khatrilab.bitbucket.org/MetaIntegratorVignette/
NEW FEATURES o Added functions related to immunoStates o Added a variety of new plotting functions for better data visualization o Added functions for power calculations, imputing sex, COCONUT conormalization, and updating gene symbols o Added LINCS integration
NEW FEATURES o This is the first development release of MetaIntegrator in Bioconductor