From: Ben Woodcroft <b.woodcroft@uq.edu.au>
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>, guix-devel@gnu.org
Subject: Re: [PATCH] gnu: Add r-centipede.
Date: Tue, 3 May 2016 09:24:08 +1000 [thread overview]
Message-ID: <5727E198.5050904@uq.edu.au> (raw)
In-Reply-To: <1462200561-19162-1-git-send-email-ricardo.wurmus@mdc-berlin.de>
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
next prev parent reply other threads:[~2016-05-02 23:24 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-05-02 14:49 [PATCH] gnu: Add r-centipede Ricardo Wurmus
2016-05-02 18:42 ` Leo Famulari
2016-05-02 18:50 ` Ricardo Wurmus
2016-05-02 23:24 ` Ben Woodcroft [this message]
2017-01-16 22:20 ` Ricardo Wurmus
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