Re: [PATCH] gnu: Add r-centipede.

[Ricardo Wurmus]

Ben Woodcroft <address@hidden> writes:

> On 03/05/16 00:49, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (r-centipede): New variable.
>> ---
>>   gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
>>   1 file changed, 21 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm 
>> b/gnu/packages/bioinformatics.scm
>> index 7d025ef..d7957cf 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -441,6 +441,27 @@ pybedtools extends BEDTools by offering feature-level 
>> manipulations from with
>>   Python.")
>>       (license license:gpl2+)))
>>
>> +(define-public r-centipede
>> +  (package
>> +    (name "r-centipede")
>> +    (version "1.2")
>> +    (source (origin
>> +              (method url-fetch)
>> +              (uri (string-append "http://download.r-forge.r-project.org/";
>> +                                  "src/contrib/CENTIPEDE_" version 
>> ".tar.gz"))
>> +              (sha256
>> +               (base32
>> +                "1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
>> +    (build-system r-build-system)
>> +    (home-page "http://centipede.uchicago.edu/";)
>> +    (synopsis "Predict transcription factor binding sites")
>> +    (description
>> +     "Centipede fits a bayesian hierarchical mixture model to learn
>> +transcription-factor-specific distribution of experimental data on a
>> +particular cell-type for a set of candidate binding sites described by a
>> +genetic motif.")
> Perhaps this is just personal opinion but I prefer not to make the
> suggestion that experiments can only be done in the lab.
>
> Also I don't think that sentence makes sense grammatically -
> s/distribution/distributions/ but even then, it doesn't learn the
> experimental data.
> Maybe steal from the website, cut down a bit from this?
>  >CENTIPEDE applies a hierarchical Bayesian mixture model to infer
> regions of the genome that are bound by particular transcription
> factors. It starts by identifying a set of candidate binding sites
> (e.g., sites that match a certain position weight matrix (PWM)), and
> then aims to classify the sites according to whether each site is bound
> or not bound by a TF. CENTIPEDE is an unsupervised learning algorithm
> that discriminates between two different types of motif instances using
> as much relevant information as possible.
>
> Thanks,
> ben

Not even a year later I pushed it to master as b91cfa22e with the
suggested change to the description.  I had totally forgotten about this
patch!

--
Ricardo

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