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Monthly Archives: February 2012
Passing arguments from the command line in Perl
I used to do this for specifying the usage: However this became a problem when I needed to pass the number “0″ as an argument. So I thought I’ll improve the code via the Perl module Getopt::Std. Depending on how … Continue reading
The Poisson distribution
The Poisson distribution
Manual linear regression analysis using R
I read a nice example in the “Statistics For Dummies” book on linear regression. The example data was the number of cricket (the insect) chirps vs. temperature. Here I redo the analysis using R. Firstly the five summaries you require … Continue reading
GC and AT content of 5′ UTRs, 3′ UTRs and coding exons of RefSeq gene models
Firstly download bed tracks of the 5′ UTR, 3′ UTR and coding exons from the UCSC Table Browser. The RefSeq gene models are in the table called RefGene. After you’ve saved the 3 bed files (e.g. mm9_refgene_090212_5_utr.bed, mm9_refgene_090212_3_utr.bed and mm9_refgene_090212_coding_exon.bed) … Continue reading
DropBox offering up to 5GB worth of space
From the official DropBox forum: During this beta period, we are also offering additional free space to test automatic uploading of photos and videos. For every 500MB of photos and videos automatically uploaded, you’ll receive another 500MB space bonus, up … Continue reading
H3K27Ac
Mainly sourced from Wikipedia but arranged as per my train of thought. Histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of … Continue reading
PCA and rggobi
I labelled only two samples since the text would overlap. Samples 1 to 20 are located near the 16 and samples 21 to 40 near the 37, as expected.
Step by step principal components analysis using R
I’ve always wondered about the calculations behind a principal components analysis (PCA). An extremely useful tutorial explains the key concepts and runs through the analysis. Here I use R to calculate each step of a PCA in hopes of better … Continue reading