eegc: Engineering Evaluation by Gene Categorization (eegc)

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
Date of publication
None
Maintainer
Xiaoyuan Zhou <zhouxiaoyuan@picb.ac.cn>
License
GPL-2
Version
1.0.0

View on Bioconductor

Man pages

barplotEnrich
Barplot the enrichResult
cate.gene
Categorized genes
categorizeGene
Gene Categorization
cate.ratio
Expression Difference ratios of categorized genes
densityPlot
Quantify Genes and Corresponding ED ratios in Each Category
diffGene
Gene Expression Differential Analysis
diffgene.genes
Differential genes for three comparisons
dotPercentage
Percentage Calculation and Visualization
eegc
eegc
enrichment
Enrichment Analysis by Hypergeometric Distribution Test
expr.filter
Filtered expression data
functionEnrich
Funtional Enrichment Analysis
goenrich
GO enrichment results
grnPlot
Gene Regulatory Network Plot
heatmapPlot
Heatmap Plot of Enriched Terms
human.gene
Gene regulatory network based human cell/tissue-specific gene...
human.grn
Human cell/tissue-specific gene-gene regulation
human.tf
Gene regulatory network based human cell/tissue-specific...
markers
Marker genes
markerScatter
Scatter Plot for Gene Expression
mouse.gene
Gene regulatory network based mouse cell/tissue-specific gene...
mouse.grn
Mouse cell/tissue-specific gene-gene regulation
mouse.tf
Gene regulatory network based mouse cell/tissue-specific...
networkAnalyze
Network Topological Analysis
SandlerFPKM
RNA-seq data in FPKM A data frame containing 16692 gene in 7...
tissueGenes
Cell/Tissue specific gene sets
tissueGroup
Tissue mapping to groups

Files in this package

eegc/DESCRIPTION
eegc/NAMESPACE
eegc/R
eegc/R/barplotEnrich.R
eegc/R/categorizeGene.R
eegc/R/densityPlot.R
eegc/R/diffGene.R
eegc/R/dotPercentage.R
eegc/R/eegc.R
eegc/R/enrichment.R
eegc/R/functionEnrich.R
eegc/R/grnPlot.R
eegc/R/heatmapPlot.R
eegc/R/markerScatter.R
eegc/R/networkAnalyze.R
eegc/README.md
eegc/build
eegc/build/vignette.rds
eegc/data
eegc/data/SandlerFPKM.rda
eegc/data/cate.gene.rda
eegc/data/cate.ratio.rda
eegc/data/datalist
eegc/data/diffgene.genes.rda
eegc/data/expr.filter.rda
eegc/data/goenrich.rda
eegc/data/human.gene.rda
eegc/data/human.grn.rda
eegc/data/human.tf.rda
eegc/data/markers.rda
eegc/data/mouse.gene.rda
eegc/data/mouse.grn.rda
eegc/data/mouse.tf.rda
eegc/data/tissueGenes.rda
eegc/data/tissueGroup.rda
eegc/inst
eegc/inst/doc
eegc/inst/doc/eegc.R
eegc/inst/doc/eegc.Rnw
eegc/inst/doc/eegc.pdf
eegc/man
eegc/man/SandlerFPKM.Rd
eegc/man/barplotEnrich.Rd
eegc/man/cate.gene.Rd
eegc/man/cate.ratio.Rd
eegc/man/categorizeGene.Rd
eegc/man/densityPlot.Rd
eegc/man/diffGene.Rd
eegc/man/diffgene.genes.Rd
eegc/man/dotPercentage.Rd
eegc/man/eegc.Rd
eegc/man/enrichment.Rd
eegc/man/expr.filter.Rd
eegc/man/functionEnrich.Rd
eegc/man/goenrich.Rd
eegc/man/grnPlot.Rd
eegc/man/heatmapPlot.Rd
eegc/man/human.gene.Rd
eegc/man/human.grn.Rd
eegc/man/human.tf.Rd
eegc/man/markerScatter.Rd
eegc/man/markers.Rd
eegc/man/mouse.gene.Rd
eegc/man/mouse.grn.Rd
eegc/man/mouse.tf.Rd
eegc/man/networkAnalyze.Rd
eegc/man/tissueGenes.Rd
eegc/man/tissueGroup.Rd
eegc/vignettes
eegc/vignettes/eegc.Rnw