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|
|Bioconductor views||DifferentialExpression GeneExpression GeneRegulation GeneSetEnrichment GeneTarget Microarray RNASeq Sequencing|
|Date of publication||None|
|Maintainer||Xiaoyuan Zhou <email@example.com>|
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
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
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