similar to: Assigning genes to CBS segmented output:

Hi, is there any package/function in Bioconductor that can do this: if given the chromosome positions of a fragment, find out all genes within, and with the information about which strand is the sense strand. And vice versa. Thanks a lot. ----- Appreciate your time & attention! -- View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html

I have a confusing error from R CMD check that I don't get when running the example manually by hand. In the \examples section of an Rd file, I create a GRanges object, then I call a function with the GRanges object, whose first 2 lines are require(GenomicRanges) annoDF <- as.data.frame(anno) # anno is the GRanges object. and that second line gives: Error in

Hi everybody, I would like to know whether it is possible to compare to tables for certain parameters. I have these two tables: gene table name chr start end str accession Length gen1 4 646752 646838 + MI0005806 86 gen12 2L 243035 243141 - MI0005821 106 gen3 2L 159838 159928 + MI0005813 90 gen7 2L

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Hi all, I''ve got overlapped and offset support in both nread and nwrite. The only thing left before I want to release this (as 0.4.0) is to get NO_BUFFERING to work. Unfortunately, I can''t get it to work. Park, I looked at that site you sent (and borrowed some code from it), but I don''t see anything special happening for NO_BUFFERING. I thought it required

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hello, I am using R 2.11.0. I have a curious problem where I get a warning in R CMD check which is seemingly not relevant to my Rd file. The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, seqLen=NULL, ...) <unescaped

Hi, I've a list containing parameters (intercepts & coefficients) of 12 regressions fitted > coeff [[1]] (Intercept) anno -427017.1740 217.0588 [[2]] (Intercept) anno -39625.82146 21.78025 ..... [[12]] (Intercept) anno 257605.0343 -129.7646 I want create a data frame with two columns (intercept and anno)using data in these list. Any help

Hello, I tried to turn lists into vectors and then bind them together in order to create a dataframe but if, after this, I try to use the function write.table I get the following error message: Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' Here is what I've done:

On Thu, Mar 19, 2015 at 12:20 PM, Sandro Bonazzola <sbonazzo at redhat.com> wrote: > Hi, > following Cloud SIG example[1] I would like to start defining the CBS tags hierarchy for Virt SIG. > > For opening the discussion I suggest: > > - virt${release}-common : packages not related to xen or kvm, used by at least 2 projects > - virt${release}-xen : xen hypervisor

On Thu, Mar 19, 2015 at 2:39 PM, Karanbir Singh <mail-lists at karan.org> wrote: > On 03/19/2015 12:23 PM, George Dunlap wrote: >> On Thu, Mar 19, 2015 at 12:20 PM, Sandro Bonazzola <sbonazzo at redhat.com> wrote: >>> Hi, >>> following Cloud SIG example[1] I would like to start defining the CBS tags hierarchy for Virt SIG. >>> >>> For

On 03/20, Sandro Bonazzola wrote: > Il 19/03/2015 15:46, George Dunlap ha scritto: > > On Thu, Mar 19, 2015 at 2:39 PM, Karanbir Singh <mail-lists at karan.org> wrote: > >> On 03/19/2015 12:23 PM, George Dunlap wrote: > >>> On Thu, Mar 19, 2015 at 12:20 PM, Sandro Bonazzola <sbonazzo at redhat.com> wrote: > >>>> Hi, > >>>>

Il 20/03/2015 11:29, Karanbir Singh ha scritto: > On 03/19/2015 02:46 PM, George Dunlap wrote: >> On Thu, Mar 19, 2015 at 2:39 PM, Karanbir Singh <mail-lists at karan.org> wrote: >>> On 03/19/2015 12:23 PM, George Dunlap wrote: >>>> On Thu, Mar 19, 2015 at 12:20 PM, Sandro Bonazzola <sbonazzo at redhat.com> wrote: >>>>> Hi,

Il 03/04/2015 08:23, Sandro Bonazzola ha scritto: > Il 19/03/2015 15:46, George Dunlap ha scritto: >> On Thu, Mar 19, 2015 at 2:39 PM, Karanbir Singh <mail-lists at karan.org> wrote: >>> On 03/19/2015 12:23 PM, George Dunlap wrote: >>>> On Thu, Mar 19, 2015 at 12:20 PM, Sandro Bonazzola <sbonazzo at redhat.com> wrote: >>>>> Hi,

Hi, please review CBS Tag Hierarchy proposed / implemented by alphacc on https://bugs.centos.org/view.php?id=8407 for aligning Virt SIG to the other SIGs. Looks ok to me. Thanks, -- Sandro Bonazzola Better technology. Faster innovation. Powered by community collaboration. See how it works at redhat.com

Just a heads-up -- 4.6.3-2, for both CentOS 7 and CentOS 6, are making their way through the build system now and should be in the mirrors hopefully sometime later this afternoon. These contain patches for XSAs 185-188, one of which is a fairly critical update, so please update as soon as they're available. -George

On 11/07/16 09:42, Timothy Lee wrote: > Dear all, > > During the course of translating the wiki into Chinese, I came across > two pages related to CBS. There is > https://wiki.centos.org/SIGGuide/CommunityBuildsystem , which was copied > from /HowTos/CommunityBuildSystem on 1 March 2016. Then there is > https://wiki.centos.org/HowTos/CommunityBuildSystem , which was last

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 07/11/2016 09:48 AM, Fabian Arrotin wrote: > AFAIK /HowTos/CommunityBuildSystem has always been the one > referenced everywhere, and then also > https://wiki.centos.org//HowTos/CommunityBuildSystem/KojiOperations > > Maybe Brian should just link to those ones, as it appears that he > copied/paste content from original page into