To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("eegc")

In most cases, you don't need to download the package archive at all.

eegc

DOI: 10.18129/B9.bioc.eegc    

This is the development version of eegc; for the stable release version, see eegc.

Engineering Evaluation by Gene Categorization (eegc)

Bioconductor version: Development (3.7)

This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic cells to primary cells based on high throughput gene expression data screened either by DNA microarray or RNA sequencing. The package takes gene expression profiles as inputs from three types of samples: (i) somatic or stem cells to be (trans)differentiated (input of the engineering process), (ii) induced cells to be evaluated (output of the engineering process) and (iii) target primary cells (reference for the output). The package performs differential gene expression analysis for each pair-wise sample comparison to identify and evaluate the transcriptional differences among the 3 types of samples (input, output, reference). The ideal goal is to have induced and primary reference cell showing overlapping profiles, both very different from the original cells.

Author: Xiaoyuan Zhou, Guofeng Meng, Christine Nardini, Hongkang Mei

Maintainer: Xiaoyuan Zhou <zhouxiaoyuan at picb.ac.cn>

Citation (from within R, enter citation("eegc")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("eegc")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("eegc")

 

PDF R Script Engineering Evaluation by Gene Categorization (eegc)
PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, RNASeq, Sequencing, Software
Version 1.5.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License GPL-2
Depends R (>= 3.3.0)
Imports R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR, DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db, org.Mm.eg.db, limma, DOSE, AnnotationDbi
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package eegc_1.5.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) eegc_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/eegc
Package Short Url http://bioconductor.org/packages/eegc/
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