Finding genes with co-expression patterns

Can the R bioconductor package "WGCNA" find artefactually created modules? Firstly some (subpar) code to generate an artefactual list of genes with co-expression patterns (modules): Running the code: ./generate_random_module.pl 10 1000 20 > 10_sample_1000_list_20_module.tsv Patterns: 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 1 1...

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RefSeq promoters

Is there any nucleotide bias with the -40 region of RefSeqs? Taking all hg19 RefSeqs that mapped to assembled chromosomes (36,004) and extracting the nucleotide sequences 40 bp upstream of the RefSeq gene model, I generated a sequence logo. No obvious TATA box enrichment, which was expected since only 10-20% of genes in eukaryotes have...

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Making a heatmap with R

Update 28th March 2017: I recommend using the superheat package for creating heatmaps. Heatmaps are great for visualising large tables of data; they are definitely popular in many transcriptome papers. Here are the basic commands for making your own heatmap: The colour schemes from the function display.brewer.all() Returning the values used for the heatmap Taken...

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Forking in Perl

Foreach item in the array, start a fork. $pid returns 0 if it is the child process. This way you can spawn 4 child processes from one parent. This page explains it all and the code shown below is an adaptation of code shown from the link. I just added code to show the current...

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