Meta-Analysis of Gene Expression Data

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.

What is this repository for?

  • This repository is for building and testing the metaIntegrator_public R package

Who do I talk to?

  • Either create an issue, email adityamr [at] stanford.edu, or email hayneswa [at] stanford.edu

How do I install the MetaIntegrator package?

For the current version on CRAN:

install.packages("MetaIntegrator")

For the current development version:

Run the following lines in R:

library(devtools)

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:

download the 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
the 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")
where PATH_TO_FILE is the path to the deapathways_1.0.tar.gz file

Documentation

To read the Vignette go to: http://khatrilab.bitbucket.org/MetaIntegratorVignette/

News

CHANGES IN VERSION 2.0.0

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

CHANGES IN VERSION 0.99.0

NEW FEATURES o This is the first development release of MetaIntegrator in Bioconductor

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("MetaIntegrator")

2.1.1 by Aditya M. Rao, 2 months ago


http://biorxiv.org/content/early/2016/08/25/071514


Browse source code at https://github.com/cran/MetaIntegrator


Authors: Winston A. Haynes , Francesco Vallania , Aurelie Tomczak , Timothy Sweeney , Erika Bongen , Aditya M. Rao , Purvesh Khatri


Documentation:   PDF Manual  


Task views: Meta-Analysis


LGPL license


Imports BiocManager, rmeta, multtest, ggplot2, parallel, Rmisc, gplots, Biobase, RMySQL, DBI, stringr, preprocessCore, GEOquery, GEOmetadb, RSQLite, data.table, ggpubr, ROCR, zoo, pracma, COCONUT, Metrics, manhattanly, DT, pheatmap, plyr, boot, dplyr, reshape2, rmarkdown, AnnotationDbi, HGNChelper, magrittr, readr, plotly, httpuv

Suggests BiocStyle, knitr, RUnit, BiocGenerics, snplist


See at CRAN