Which Bioconductor packages?

Question

[tfhahn]

What are the best Bioconductor packages to create networks, analyze time series data? Analyzing promoter regions? Predicting Tanscription Factor and their Binding Sites? Predicting interventions to extend lifespan without being able to work kin a wet-lab? What is the fastest way to quickly get publications in genomics or bioinformatics despite limited training? How can one find something novel without having access to one's own dataset? What is easier to learn for networks? iGraph or Cytoscape?

[Jean-Karim Heriche]

You should create one post per question, each with a relevant title. This keeps things organized.

How can one find something novel without having access to one's own dataset ?

That doesn't make much sense to me. What do you work on if you don't have data ?

Answer 1

[tfhahn]

For my masters my adviser gave me a microarray dataset to analyze that nobody else had access to. So it was certain that I would be able to find something new because I was the only one, who had access to the dataset. But now we don't have money for generating microarray or RNA Seq datasets, but still I somehow need to find some new before I can graduate but that is so much harder now. And my school has no more funding and therefor urged me to hurry up and graduate. But I am still looking for ideas for writing my proposal since all the results I had so far were only transient, i.e. I thought I had results until I found out later that they are not true permanent results because the more you know the more exceptions one gets aware of.

[WouterDeCoster]

Please used ADD REPLY to answer to earlier reactions, as such this thread remains logically structured and easy to follow.