Gene-Expression-SecondaRy-Analysis

Repository of R scripts for analysis of gene expression data in either FPKM matrix or count matrix format.

Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
SettingsFiles		SettingsFiles
shell-scripts		shell-scripts
.Rhistory		.Rhistory
BioNet-and-graphite-network-analysis.R		BioNet-and-graphite-network-analysis.R
Cuffdiff-Secondary-Analysis-BIOL607.Rmd		Cuffdiff-Secondary-Analysis-BIOL607.Rmd
Cuffdiff-Secondary-Analysis-Organized-BIOL607-Project.Rmd		Cuffdiff-Secondary-Analysis-Organized-BIOL607-Project.Rmd
DecisionTrees.R		DecisionTrees.R
EGSEAWorkflow.R		EGSEAWorkflow.R
EGSEAWorkflow.Rmd		EGSEAWorkflow.Rmd
README.RNA-Seq-notes.md		README.RNA-Seq-notes.md
README.md		README.md
RNA-Seq-Decision-Trees.R		RNA-Seq-Decision-Trees.R
S_meliloti_GO_analysis_rsubread-data.R		S_meliloti_GO_analysis_rsubread-data.R
Tailor RNA-Seq Pipeline R Code.Rmd		Tailor RNA-Seq Pipeline R Code.Rmd
Tailor-CharacteristicSubnetworkDiscovery.Rmd		Tailor-CharacteristicSubnetworkDiscovery.Rmd
Tailor-RNA-Seq-Analysis-Cuffdiff-EdgeR-Limma.Rmd		Tailor-RNA-Seq-Analysis-Cuffdiff-EdgeR-Limma.Rmd
The_Tailor_RNA-Seq_Diff-Expr_Pipeline_for_Biomarker_Discovery.Thesis.Rmd		The_Tailor_RNA-Seq_Diff-Expr_Pipeline_for_Biomarker_Discovery.Thesis.Rmd
Urine1 RNA-Seq Differential Expression Notebook.Rmd		Urine1 RNA-Seq Differential Expression Notebook.Rmd
Voom-edgeR-DESeq-bayseq-examples.R		Voom-edgeR-DESeq-bayseq-examples.R
bionet.R		bionet.R
caret.Rmd		caret.Rmd
correlation_matrix.R		correlation_matrix.R
cummeRbund-golplots-igraph.R		cummeRbund-golplots-igraph.R
cummeRbund.R		cummeRbund.R
deseq-vs-edger.R		deseq-vs-edger.R
edgeR-glm-analysis.R		edgeR-glm-analysis.R
glmqlftest_edger.R		glmqlftest_edger.R
gmt2gs.R		gmt2gs.R
go.R		go.R
goplots.R		goplots.R
human-interactome-network-analysis.R		human-interactome-network-analysis.R
limmaWorkflow.Rmd		limmaWorkflow.Rmd
pathview.R		pathview.R
pathview.retry.R		pathview.retry.R
plotNetworksRcytoscape.R		plotNetworksRcytoscape.R
tailor-network-script-using-igraph.R		tailor-network-script-using-igraph.R
tcell-net.R		tcell-net.R
vennDiagram_leavout.R		vennDiagram_leavout.R

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