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.

AuthorXiaoyuan Zhou, Guofeng Meng, Christine Nardini, Hongkang Mei
Date of publicationNone
MaintainerXiaoyuan Zhou <zhouxiaoyuan@picb.ac.cn>
LicenseGPL-2
Version1.0.0

View on Bioconductor

Functions

barplotEnrich Man page
cate.gene Man page
categorizeGene Man page
cate.ratio Man page
densityPlot Man page
diffGene Man page
diffgene.genes Man page
dotPercentage Man page
eegc Man page
eegc-package Man page
enrichment Man page
expr.filter Man page
functionEnrich Man page
goenrich Man page
grnPlot Man page
heatmapPlot Man page
human.gene Man page
human.grn Man page
human.tf Man page
markers Man page
markerScatter Man page
mouse.gene Man page
mouse.grn Man page
mouse.tf Man page
networkAnalyze Man page
SandlerFPKM Man page
tissueGenes Man page
tissueGroup Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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