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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. http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info

websites:

GUI informatics tools:(non-programmers)
ChIP-seq tools based on Galaxy developed by shirley Liu in harvard Cisgenome http://cistrome.dfci.harvard.edu/Cistrome/Cistrome_Project.html
Genome space http://www.genomespace.org/  if you really do not want to learn how to program, use it.
SeqMonk http://www.bioinformatics.babraham.ac.uk/projects/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 http://www.broadinstitute.org/igv/


resources:
NCBI GEO datasets: http://www.ncbi.nlm.nih.gov/  
cBio Cancer Genomics Portal http://www.cbioportal.org/public-portal/
Roadmap epigenetics http://roadmapepigenomics.org/
David pathway analysis  http://david.abcc.ncifcrf.gov/
KEGG pathway analysis http://www.genome.jp/kegg/

free online courses https://www.coursera.org/  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 http://www.r-project.org/ ,Bioconductor is based on R http://www.bioconductor.org/, there are many packages there also, just take time to learn.

SeqAnswer http://seqanswers.com/ 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 http://code.google.com/p/bpbio/
mysql 

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