Comments for >_rg::lab http://www.rglab.org Raphael Gottardo's Research Lab Thu, 29 Sep 2011 17:30:35 +0000 hourly 1 http://wordpress.org/?v=3.3.1 Comment on PICS: Probabilistic Inference for ChIP-Seq by Raphael Gottardo http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-20405 Raphael Gottardo Thu, 29 Sep 2011 17:30:35 +0000 http://www.rglab.org/?p=228#comment-20405 Carlos, Thanks for your kind message. We are about to release PING for nucleosome positioning. We have just submitted it to Bioconductor. We'll keep you posted. Raphael Carlos,

Thanks for your kind message. We are about to release PING for nucleosome positioning.
We have just submitted it to Bioconductor. We’ll keep you posted.

Raphael

]]> Comment on PICS: Probabilistic Inference for ChIP-Seq by Carlos Torroja http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-20332 Carlos Torroja Fri, 23 Sep 2011 14:09:02 +0000 http://www.rglab.org/?p=228#comment-20332 Hi! I've been using your PICS and rGADEM packages with fantastic results. I've been comparing it with MACS with high coverage experiments and it definitively outperformed MACS. Now I'm working with Histone Chip-Seq experiments and I would like to know whether the PICS development version 1.7.0 includes already the Histone specific settings. I couldn't figure out from the documentation as it is not updated yet. I'm considering other packages as ChIPseqR or PeakRanger, but I would like to compare them with PICS. Will you describe somewhere what did you considered and changed in you algorithm to deal with Histone peaks? Also I had some issues with PICS that I would like to discuss. Is this the right place to do it? Thanks a lot for your fantastic software. Carlos Hi! I’ve been using your PICS and rGADEM packages with fantastic results. I’ve been comparing it with MACS with high coverage experiments and it definitively outperformed MACS.

Now I’m working with Histone Chip-Seq experiments and I would like to know whether the PICS development version 1.7.0 includes already the Histone specific settings. I couldn’t figure out from the documentation as it is not updated yet. I’m considering other packages as ChIPseqR or PeakRanger, but I would like to compare them with PICS.

Will you describe somewhere what did you considered and changed in you algorithm to deal with Histone peaks?

Also I had some issues with PICS that I would like to discuss. Is this the right place to do it?

Thanks a lot for your fantastic software.

Carlos

]]> Comment on PICS: Probabilistic Inference for ChIP-Seq by Raphael Gottardo http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-18682 Raphael Gottardo Tue, 22 Feb 2011 20:48:13 +0000 http://www.rglab.org/?p=228#comment-18682 Should be soon. We will submit a version to Bioconductor in the next couple of weeks. Should be soon. We will submit a version to Bioconductor in the next couple of weeks.

]]> Comment on PICS: Probabilistic Inference for ChIP-Seq by Fabiano http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-18677 Fabiano Tue, 22 Feb 2011 04:32:49 +0000 http://www.rglab.org/?p=228#comment-18677 Hi there When do you release your PICS with histone modification option? Is it in the next release of Bioconductor (when is this?!) or sooner? Thanks Fabiano Hi there

When do you release your PICS with histone modification option? Is it in the next release of Bioconductor (when is this?!) or sooner?

Thanks

Fabiano

]]> Comment on PICS: Probabilistic Inference for ChIP-Seq by Raphael Gottardo http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-18608 Raphael Gottardo Tue, 08 Feb 2011 17:20:00 +0000 http://www.rglab.org/?p=228#comment-18608 Hi Rebecca, Everything should be on our wiki: wiki.rglab.org. Please let me know if you have any questions. Raphael Hi Rebecca,

Everything should be on our wiki: wiki.rglab.org. Please let me know if you have any questions.

Raphael

]]> Comment on PICS: Probabilistic Inference for ChIP-Seq by Rebecca http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-18600 Rebecca Mon, 07 Feb 2011 17:09:59 +0000 http://www.rglab.org/?p=228#comment-18600 Hi there, I am eager to try out PICS! Please can you send me the link to the mappability profiles and scripts mentioned by George please, I can't find them!? Thank you very much, Rebecca Hi there,

I am eager to try out PICS! Please can you send me the link to the mappability profiles and scripts mentioned by George please, I can’t find them!?

Thank you very much,

Rebecca

]]> Comment on GSL and 64 bit windows by Raphael Gottardo http://www.rglab.org/2010/05/gsl-and-64-bit-windows/comment-page-1/#comment-18158 Raphael Gottardo Sun, 02 Jan 2011 16:39:17 +0000 http://www.rglab.org/?p=535#comment-18158 Hi Asim, I can't remember, I have asked Arnaud Droit who should be able to answer soon. Cheers, Raphael Hi Asim,

I can’t remember, I have asked Arnaud Droit who should be able to answer soon.

Cheers,

Raphael

]]> Comment on GSL and 64 bit windows by Asim http://www.rglab.org/2010/05/gsl-and-64-bit-windows/comment-page-1/#comment-18123 Asim Sat, 01 Jan 2011 00:23:31 +0000 http://www.rglab.org/?p=535#comment-18123 Which compiler do you use with the 64 bit binaries for Windows? Thanks Asim Which compiler do you use with the 64 bit binaries for Windows?

Thanks

Asim

]]> Comment on PICS: Probabilistic Inference for ChIP-Seq by Raphael Gottardo http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-17573 Raphael Gottardo Fri, 10 Dec 2010 04:27:24 +0000 http://www.rglab.org/?p=228#comment-17573 Hi George, Sorry, we've been a bit slower than expected but it's coming. If it's not out by mid January, we will send you a beta! Cheers, Raphael Hi George,

Sorry, we’ve been a bit slower than expected but it’s coming. If it’s not out by mid January, we will send you a beta!

Cheers,

Raphael

]]> Comment on PICS: Probabilistic Inference for ChIP-Seq by George Allen http://www.rglab.org/2009/03/pics-probabilistic-inference-for-chip-seq/comment-page-1/#comment-17572 George Allen Fri, 10 Dec 2010 03:20:59 +0000 http://www.rglab.org/?p=228#comment-17572 Hi Raphael Thanks for putting up the mappability profiles and scripts! Just wondering if there's an update on when the 'histone' version of PICS will be available. I'm eager to put it in a pipeline I'm setting up but, ideally, would like to be analysing data by mid January so it would be useful to know if I should be implementing something else in the interim if you're estimated release date is much later than that. Many thanks in advance George Hi Raphael

Thanks for putting up the mappability profiles and scripts! Just wondering if there’s an update on when the ‘histone’ version of PICS will be available. I’m eager to put it in a pipeline I’m setting up but, ideally, would like to be analysing data by mid January so it would be useful to know if I should be implementing something else in the interim if you’re estimated release date is much later than that.

Many thanks in advance

George

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