## User: Charles Berry

Charles Berry290
Reputation:
290
Status:
Trusted
Location:
United States
Last seen:
3 months, 2 weeks ago
Joined:
16 years, 8 months ago
Email:
c******@ucsd.edu

Professor Emeritus of Biostatistics and Bioinformatics

Current interest: statistical models, methods, and software for exploring populations of integration sites such as occur in retroviral infections or in gene therapies using retrovirus-like constructs.

#### Posts by Charles Berry

<prev • 30 results • page 1 of 3 • next >
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... biovizBase. example("getIdeoGR" ) is a start. ...
written 3 months ago by Charles Berry290
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... ave() will give the sequential numbers, so something like with(mydf, paste0(ID, ave( ID, ID, FUN=seq_along ))) should do it.   ...
written 3.9 years ago by Charles Berry290
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... No. There was a post on bio-devel. Try remove.packages("BiocInstaller"). Then start over. ...
written 4.3 years ago by Charles Berry290
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... On Fri, 11 Jul 2014, Martin Morgan wrote: > On 07/10/2014 02:45 PM, Charles Berry wrote: >> >> I'd like to be able to specify the starting 'centers' for dmn(). >> [snip] > I'll look into this, thanks for the suggestion. Is there a more general issue > that makes the ran ...
written 5.0 years ago by Charles Berry290
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... I'd like to be able to specify the starting 'centers' for dmn(). Details: IIUC DirichletMultinomial::dmn(count, k) will initialize the EM algorithm using a kmeans heuristic for selecting the starting point. Replicate runs on the same data can yield stark differences in the result. I have a datas ...
written 5.0 years ago by Charles Berry290 • updated 5.0 years ago by Martin Morgan ♦♦ 23k
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... Michael Lawrence writes: > Thanks for your reply and for GenomicRanges. Please see inline comments below. > > On Tue, Jan 7, 2014 at 9:30 AM, Charles Berry wrote: > > > Vince S. Buffalo ...> writes: > > > > > > > > Hi Bioconductor folks, > > ...
written 5.5 years ago by Charles Berry290 • updated 5.5 years ago by Michael Lawrence11k
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... Vince S. Buffalo writes: > > Hi Bioconductor folks, > > I'm trying to create some GRanges summaries, but I think I may be missing > an obvious solution. I have fixed-width windows as a GRanges object, and > for each window/row I'd like to add a metadata column that indicates how ...
written 5.5 years ago by Charles Berry290 • updated 5.5 years ago by Michael Lawrence11k
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... Peter Hickey writes: > > Hi all, > > Suppose I've created a Hits object by > all_hits <- findOverlaps(query, subject, select = 'all', type = 'any') > and now I want to get the first (or last) hit for each query. Of course, > [...] gr1 <- GRanges(rep(letters,each=10), ...
written 5.8 years ago by Charles Berry290
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... Ludo Pagie writes: > > Hi all, > > I don't understand what's going on here.I'm trying to compute the > coverage of a few ranges. I specify a weight for these ranges and for > some positions I get a coverage even though I know these positions are > only covered by ranges which ...
written 5.9 years ago by Charles Berry290
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... Valerie Obenchain writes: > > Hi Andrew, > > I can't reproduce this problem. Can you successfully save the files in a > different order, i.e., is it just the addition of 'introns' that is > giving you trouble? > > I assume these are custom annotation GRanges that did not co ...
written 5.9 years ago by Charles Berry290

#### Latest awards to Charles Berry

Popular Question 3.9 years ago, created a question with more than 1,000 views. For Most efficient way to compute width of overlap of multiple features
Autobiographer 4.7 years ago, has more than 80 characters in the information field of the user's profile.

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