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
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Engineering Evaluation by Gene Categorization (eegc)
Bioconductor version: Release (3.5)
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")
| R Script | Engineering Evaluation by Gene Categorization (eegc) | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneRegulation, GeneSetEnrichment, GeneTarget, Microarray, RNASeq, Sequencing, Software |
| Version | 1.2.0 |
| 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_1.2.0.tar.gz |
| Windows Binary | eegc_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | eegc_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/eegc |
| Package Short Url | http://bioconductor.org/packages/eegc/ |
| Package Downloads Report | Download Stats |
Documentation »
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