Package: eegc
Type: Package
Title: Engineering Evaluation by Gene Categorization (eegc)
Version: 1.30.0
Date: 2018-12-21
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 (>= 3.4.0)
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: ImmunoOncology, Microarray, Sequencing, RNASeq,
        DifferentialExpression, GeneRegulation, GeneSetEnrichment,
        GeneExpression, GeneTarget
License: GPL-2
LazyData: TRUE
RoxygenNote: 5.0.1
PackageStatus: Deprecated
git_url: https://git.bioconductor.org/packages/eegc
git_branch: RELEASE_3_19
git_last_commit: d61283d
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: no
Packaged: 2024-05-01 22:38:02 UTC; biocbuild
Built: R 4.4.0; ; 2024-05-02 12:46:04 UTC; windows
