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Tool:CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
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4.7 years ago
dvelmeshev • 0

Dear users,

If you deal with RNA sequencing data analysis, please take a look at CANEapp , a new application developed by our team at University of Miami:
http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app

The uniqueness of CANEapp is that it allows you to perform analysis of RNA-seq data without the need of using the terminal or passing commands to the server and completely automated the analysis process. The user interface runs on your personal computer and connects to the server, where an automated algorithm takes care of the analysis. Therefore, it can be of interest for pure biologists, as well as for bioinformatitians as a tool for RNA-seq analysis automation.

If you are interested read the CANEapp paper:
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2346-y

If you have questions, suggestions, detect bugs or experience problems, please email me (Dmitry) or visit our Google Group:
https://groups.google.com/d/forum/caneapp

CANEapp is an open-source program; the source code is here:
https://github.com/DmitryVel/CANEapp

RNA-Seq Tool • 1.2k views
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I appreciate the current title, which looks like you're advertising yourself as being a tool :P

N.B., I'll modify the title for you :)

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Thank you Devon, I guess I missed that! :)

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What are the benefits relative to other tools that do the same thing, such as Galaxy?

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Indeed, the description of Galaxy in the paper is incorrect. Steps in a "workflow" are automated and can even be shared between users and installed from the tool shed. There's also a trivial installation of Galaxy with docker (I manage a couple instances of that) and it offers a large number of alternative workflows.

Having said that, if people just need RNAseq-related stuff then a dedicated application might be simpler.

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Right on - I was thinking of cases when a certain experiment might require a bit of tweaking. Seems easy to do in Galaxy, but less so for hard-coded applications. Colleagues/graduate students who have little or no programming experience have found the ability to switch things up pretty convenient.

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CANEapp is in no way a competitor/alternative to Galaxy and has a different target audience.

The idea of the application is to allow biologists to analyze their RNA-seq data without a bioinformatics support. Utilizing production Galaxy requires such support, which is not always available.

The idea was born through working with biologists that tried many tools, including Galaxy, but were not satisfied by them.

Of course due to its structure Galaxy allows far more flexibility but not as easily accessible by pure biologists.

I intend to continue working on CANEapp in the future to enable more tools and tweaking while maintaining simplicity of usage, automation and full accessibility by biologists.

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Hi Bruce,

CANEapp is fully automated, does not require installation and works on multiple Linux systems, meaning it can be easily used on a server for large-scale analysis. There is zero requirement to pass commands to server through a terminal, install dependencies etc. You download the application and run.

Galaxy is a great tool but suggests (some) knowledge of workflows and individual tools (such as Tophat). Moreover, to use Galaxy on a server for large-scale analysis, it has to be installed, which is not easy to do for researchers with no computational background.

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Isn't the fact that these tools, such as Galaxy, require some knowledge of the actual methods being performed a good thing? I am leery of inexperienced researchers simply clicking 'go' on an analysis and introducing methodological biases because they don't know the assumptions of the techniques/models they're applying.

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