Meeting Mo 28th April ?

[Kevin Rue]

Hi all,

Who would like to have a meeting next Monday?

I would like to present, demonstrate and get opinions on a R package I have developed over the past week (called anovaGO for the time being, but may change if it moves on to publication). Also, I would like to present it at the VIBE meeting in Carlow on the 5th of May, and the OpenSeq group is a very good place to train myself for that sort of meetings.

In a sentence, the package identifies GO terms enriched in genes clustering best samples according to a given factor (e.g. "Treatment"). 

A lot like many pathway analyses tools out there, except for the added value of built-in heatmap, hierarchical clustering, and gene expression profile visualisation functions, once the GO terms and genes of interest 

The current release only support RNA-seq data, but I just finished writing some unrelease code that support microarray data too.

Cheers

Kevin

Some additional remarks:

The demonstration would be much more interactive if one of you would bring one of their own datasets. If possible from a species in the BioMart database but that is not Bos taurus. As described in the example workflow (https://github.com/kevinrue/anovaGO/wiki/Typical-analysis-pipeline) I need only two variables:

• log2cpm a sample-by-gene matrix providing the expression level of each gene (rows; ensembl gene identifiers expected) in each sample (columns). In this example, we consider log2-transformed counts per million data obtained from RNA-sequencing after normalisation by the library size and filtering of lowly expressed genes (e.g. edgeR)
• targets an AnnotatedDataFrame (from the Biobase package) providing phenotypic information about the samples. Row names are samples, column names must include at least one factor (in the R meaning) with two or more levels (in the R meaning). Additional factors and phenotypic traits can be present in other columns and used later to re-label the samples in the heatmap and hierarchical clustering plots. In this example, we assume the presence of a column named "Treatment" which has three levels (e.g. "Control", "Low", and "High"), another column named "Timepoint" which has four levels (e.g. "2", "6", "24", and "48" as numeric values), and one last column named "Animal" with 10 levels (e.g. "A1", "A2", ..., "A10").

Those who would like to know what my package is about are welcome to browse its GitHub (https://github.com/kevinrue/anovaGO), download and test the latest release (https://github.com/kevinrue/anovaGO/releases)  following the example workflow (https://github.com/kevinrue/anovaGO/wiki/Typical-analysis-pipeline), and browse the Wiki (https://github.com/kevinrue/anovaGO/wiki) for additional help.

The package also comes with vignettes documenting the API.

Cheers

Kevin

--

Kévin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en

[Nicolas Nalpas]

Hey Kevin,

 

Sounds good, depending on everyone else, I am good for the 28^th J

Thanks,

Nicolas

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[Karsten Hokamp]

Hi Kevin,

You can count me in as well, 

      Karsten

[Lisa Rogers]

Sounds interesting Kevin.  I'll be there as well, though I don't have any relevant data to bring. 

[Kevin Rue]

Cool Lisa, thanks for the email !

By the way, auick update: for "marketing" purposes I decided to rename the package "GOexpress", therefore:

• GitHub located at https://github.com/kevinrue/GOexpress
• Wiki located at https://github.com/kevinrue/GOexpress/wiki
• etc etc..

I am currently updating all the package files to replace anovaGO by GOexpress. The renamed package will be available directly as GOexpress release 0.5.1 on GitHub.

The external dataset I mentioned for the meeting would most of all be interesting for me to test the ease to feeds someone else's data into my software, instead of the my own data which has been validated many times during the tests.

If someone feels like preparing those two variables for Monday, the great, otherwise, we can easily have the meeting without. I have everything prepared on static slides anyway, although I will demonstrate the software in real time afterwards to get your opinion.

Cheers

Kevin

On 24 April 2014 16:37, Lisa Rogers <lisa.r...@ucdconnect.ie> wrote:

Sounds interesting Kevin.  I'll be there as well, though I don't have any relevant data to bring. 

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[Kevin Rue]

Hi all,

Quick reminder for the OpenSeq meeting today at 2pm in the Conway Interactive Hub.

Best,

Kevin