[Bioc-devel] I would like to publish a bioconductor package.

Hervé Pagès hpages at fhcrc.org
Wed Feb 27 18:39:24 CET 2013

Hi Davide,

Please refer to this page for how to submit your package:




On 02/27/2013 08:25 AM, Stephanie M. Gogarten wrote:
> You can solve the package size issue by putting your example data in a
> separate "experiment data" package
> (http://www.bioconductor.org/packages/release/data/experiment/).
> Stephanie
> On 2/27/13 3:03 AM, Davide Rambaldi wrote:
>> Hi all,
>> I am working on a library called flowFit, the purpose of this library
>> is to analyze the FACS data coming from proliferation tracking dyes
>> study.
>> The library depends on the flowCore and flowViz bioconductor libraries
>> and use minpack.lm (levenberg-marquadt algorithm) to fit a set of
>> peaks over the FACS data.
>> A typical experimental pipeline:
>> 1) Acquire with FACS a sample of unlabelled cells
>> 2) Acquire with FACS a sample of labeled and unstimulated cells (the
>> Parent Population)
>> 3) Acquire with FACS a sample of labeled and stimulated cells (the
>> Proliferative Population)
>> In R we can use the flowCore functions to transform the raw data and
>> to gate the population of interest. Once we have gated the correct
>> population, with 2 commands of flowFit you can perform the fitting:
>>> library(flowFit)
>>> parent <- parentFitting(QuahAndParish[[1]], "<FITC-A>")
>>> fitting <- proliferationFitting(QuahAndParish[[2]],  "<FITC-A>",
>>> parent.fitting.cfse at parentPeakPosition,
>>> parent.fitting.cfse at parentPeakSize)
>> The function can generate also some graphical output with:
>>> plot(fitting.cfse)
>> To demonstrate the correctness of the fitting I have made some in
>> silico simulations and a retrospective analysis of the data from the
>> paper:
>> "New and improved methods for measuring lymphocyte proliferation in
>> vitro and in vivo using CFSE-like fluorescent dyes", Benjamin J.C.
>> Quah ⁎, Christopher R. Parish, Journal of Immunological Methods (2012)
>> In this paper, the same population of lymphocytes (proliferation with
>> the same growth conditions) was stained with 3 different proliferation
>> tracking dyes: if the fitting algorithm is working as expected, we
>> expect to estimate the same % of cells for generation in the 3 sample.
>> Comparing the 3 samples we didn't see any significant difference in
>> the estimation of the % of cell for generations, suggesting us that
>> the algorithm is correctly estimating the % of cells / generation.
>> I have posted a graphical output example with the Quah and Parish data
>> (pdf) here:
>> http://dl.dropbox.com/u/40644496/QuahAndPArishOut.pdf
>> The dataset will be included in the library (in the data subdir).
>> Actually I am writing the vignette (I am following the guidelines in
>> http://www.bioconductor.org/developers/package-guidelines/) and fixing
>> some graphical bugs (like the legend oversized …).
>> The package Pass R CMD build and R CMD CHECK (time: 86 seconds) with
>> no errors on OSX and Linux (I have to find a windows machine somewhere
>> ...), I still have to test with the R-devel version of R.
>> The library is bigger than expected (4.2 Mb) because the example
>> datasets (FCS files converted in .Rdata) are big (3.7M) and I don't
>> know how to solve this issue...
>> My question is, How I proceed from here?
>> I would like to publish the library/methods in a paper (Bioinformatics
>> Journal may be?) and submit the library to Bioconductor, which is the
>> correct way to proceed?
>> Thanks
>> P.S: If I miss (again!) some FAQ please apologize me
>> -----------------------------------------------------
>> Davide Rambaldi, PhD.
>> -----------------------------------------------------
>> IEO ~ MolMed
>> [e] davide.rambaldi at ieo.eu
>> [e] davide.rambaldi at gmail.com
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> _______________________________________________
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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