Network-analysis

This repository contain materials used to develop a gene co-expression network, to decipher pathogenesis of Rift Valley Fever in Bos taurus_

Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
.Rhistory		.Rhistory
.TOM101.R.swi		.TOM101.R.swi
.TOM101.R.swj		.TOM101.R.swj
.TOM101.R.swk		.TOM101.R.swk
.TOM101.R.swm		.TOM101.R.swm
.TOM101.R.swn		.TOM101.R.swn
.TOM101.R.swo		.TOM101.R.swo
.TOM101.R.swp		.TOM101.R.swp
.annot.swp		.annot.swp
.annotation.swo		.annotation.swo
.annotation.swp		.annotation.swp
.gitignore		.gitignore
.network101.R.swo		.network101.R.swo
.network101.R.swp		.network101.R.swp
.newcript.R.swp		.newcript.R.swp
.ontology.swp		.ontology.swp
.overrepresentation.swp		.overrepresentation.swp
.scam.R.swp		.scam.R.swp
Adjacency matrix.pdf		Adjacency matrix.pdf
Combined_script.R		Combined_script.R
Gene dendrogram and module colors.pdf		Gene dendrogram and module colors.pdf
NA.txt		NA.txt
Network-analysis.Rproj		Network-analysis.Rproj
README.md		README.md
Similarity matrix.pdf		Similarity matrix.pdf
SraRunTable.csv		SraRunTable.csv
TOM101.R		TOM101.R
TOM101.R.save		TOM101.R.save
analysis (1).Rmd		analysis (1).Rmd
annot		annot
annotation		annotation
code.R		code.R
density plots.pdf		density plots.pdf
drosphila_example_de.csv		drosphila_example_de.csv
filtered.counts.RDS		filtered.counts.RDS
log2-transformed.pdf		log2-transformed.pdf
logcpm.norm.counts.RDS		logcpm.norm.counts.RDS
logcpm.unnorm.counts.RDS		logcpm.unnorm.counts.RDS
metadata.R		metadata.R
metadata.csv		metadata.csv
metadata.txt		metadata.txt
module colors and the number of genes in each.Rnw		module colors and the number of genes in each.Rnw
module_colors.csv		module_colors.csv
module_colors.pdf		module_colors.pdf
module_labels.csv		module_labels.csv
module_table.PNG		module_table.PNG
network.R		network.R
network101.R		network101.R
read.counts.RDS		read.counts.RDS
sample_check.R		sample_check.R
sample_correlation_pre_filtering.pdf		sample_correlation_pre_filtering.pdf
samples.metadata.RDS		samples.metadata.RDS
scale-free topology.pdf		scale-free topology.pdf

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