User: mattia pelizzola

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Posts by mattia pelizzola

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[JOB] NGS and computational genomics postdoc positions
... Hi, several post-doctoral positions are available in the Computational Epigenomics unit at the Center for Genomic Science of IIT@SEMM ( http://genomics.iit.it/groups/computational-epigenomics.html), a new outstation of the Italian Institute of Technology located in the IFOM- IEO Campus in Milan (h ...
cancer written 5.9 years ago by mattia pelizzola200
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Computational Biologist position available in Screening Unit in Milan, Italy
... Computational Biologist position available in Screening Unit in Milan, Italy: http://www.iit.it/en/resources/openings/iit-centres/iitsemm /computational-biologist-semm.html IIT at SEMM is a research outstation of the Fondazione Istituto Italiano di Tecnologia located in Milan at the IFOM-IEO-CAMP ...
cancer written 6.5 years ago by mattia pelizzola200
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4 PhD positions in cancer computational biology
... Dear all,* * enrollment is open for 4 PhD positions in cancer computational biology at the IFOM-IEO campus in Milan, see the ad below. Best, mattia ** *############################# * * * *Cancer computational biology* Four PhD positions in Computational Biology are available at the I ...
sequencing epigenetics cancer written 6.6 years ago by mattia pelizzola200
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PhD program in Computational Biology in Milan, Italy
... *Applications are solicited for a PhD program in Computational Biology in Milan, Italy:* * * *Epigenome evolution in tumor models* (*Amati group, IIT & IEO*) Cancer originates from a complex combination of alterations at the level of the genome as well as of the epigenome. We are using next-ge ...
chipseq written 6.7 years ago by mattia pelizzola200
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occurrence of rGADEM motifs
... Hi, I am using rGADEM and MotIV to find out enriched motifs in my ChIPseq peaks and determine the similarity with Jaspar TFBS. These tools look very useful! rGADEM provides a list of enriched motifs. The total number of motifs is provided by the nOccurrences function, but I can't find a way to get ...
rgadem motiv written 6.7 years ago by mattia pelizzola200 • updated 6.7 years ago by Charles Joly Beauparlant160
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rtracklayer issues with other packages?
... Hi Martin, I am back on this rtracklayer issue after a while. There is a bug specifically when the package graph is loaded too (before or after rtracklayer). The code (apart from library(graph)) is from the rtracklayer vignette: > library(graph) > library(rtracklayer) Loading required packag ...
go cancer bsgenome graph biostrings gostats rtracklayer written 7.4 years ago by mattia pelizzola200 • updated 7.4 years ago by Michael Lawrence10.0k
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rtracklayer issues with other packages?
... Hi, I am running some code from the rtracklayer vignette. If I start a new R session and I load the rtracklayer only, the code works fine. Unfortunately, I need many other packages at the same time. For some reason when loading all the other packages I get this error: > data(targets) > targe ...
go bsgenome rtracklayer written 7.8 years ago by mattia pelizzola200 • updated 7.8 years ago by Martin Morgan ♦♦ 21k
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Comment: C: snow library, question on clusterExport
... thanks Martin for the explanations and thanks Norman for pointing out that error in the example, unfortunately I am still stuck with the main problem: I have to use clusterExport to export an object to the cluster nodes. clusterExport only seems to export objects from the GlobalEnv, unfortunately. ...
written 8.0 years ago by mattia pelizzola200
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snow library, question on clusterExport
... Hi, I have a simple function: > library(snow) > fun2=function() { + cl=makeCluster(3) + Mat=matrix(2:10,3,3) + fun3=function(startInd, endInd=3, data=Mat) {Mat[startInd:endInd,]} + print(clusterApplyLB(cl, 1:3, fun3)) + stopCluster(cl) + } that is working fine: > fun2() [[1]] [,1] ...
written 8.0 years ago by mattia pelizzola200 • updated 8.0 years ago by Pavelka, Norman70
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autocorrelation analysis
... Hi, I am trying to get some autocorrelation analysis based on positions of DNA words. Given a certain DNA motif or word, you can have its positions on the genome. I am trying to figure out if there is any regularity (pattern) in that. What I did is to determine pair-wise distances and see how many ...
written 8.9 years ago by mattia pelizzola200 • updated 8.9 years ago by Zeljko Debeljak50

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