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Wednesday, April 3, 2013

Bioinformatics resources

operation system: google Bio-liunx you will find it and you can install it for free. If you use mac, you may consider to have a dual booting system or use a virtual machine.


GUI informatics tools:(non-programmers)
ChIP-seq tools based on Galaxy developed by shirley Liu in harvard Cisgenome
Genome space  if you really do not want to learn how to program, use it.
SeqMonk it is a great tool to analysis ChIP-seq, RNA-seq, Hi-C data
and can generate beautiful graphs. sometimes I am just too lazy to program by myself :) why not use the existing tools?
you can use it as a local Genome browser, or you can try IGV for an alternative

NCBI GEO datasets:  
cBio Cancer Genomics Portal
Roadmap epigenetics
David pathway analysis
KEGG pathway analysis

free online courses  I took several python classes there, great! 
I recommend the following courses for you, take them in order. You may have missed the class, but you can still log in and 
watch the videos.

Learn to Program: The Fundamentals

If you use R ,Bioconductor is based on R, there are many packages there also, just take time to learn.

SeqAnswer good place to ask questions and get update of the current sequencing trend.

linux command line based for sequencing data manipulation (try to switch to linux, I am sure you will love it:) :
simple bioinformatics script

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