Package: eegc
Type: Package
Title: Engineering Evaluation by Gene Categorization (eegc)
Version: 1.0.0
Date: 2016-08-20
Author: Xiaoyuan Zhou, Guofeng Meng, Christine Nardini, Hongkang Mei
Maintainer: Xiaoyuan Zhou <zhouxiaoyuan@picb.ac.cn>
Description: 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.
VignetteBuilder: knitr
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
Suggests: knitr
biocViews: Microarray, Sequencing, RNASeq, DifferentialExpression,
        GeneRegulation, GeneSetEnrichment, GeneExpression, GeneTarget
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-10-18 00:45:41 UTC; biocbuild
Built: R 3.3.1; ; 2016-10-18 02:10:53 UTC; windows
