User: Tim Triche

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Tim Triche4.2k
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Website:
http://trichelab.vai.org/
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@timtriche
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Joined:
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Assistant Professor of Bioinformatics, Van Andel Research Institute

Adjunct Professor of Translational Genomics, University of Southern California

Founding Partner, Anamnesis LLC

 

Posts by Tim Triche

<prev • 429 results • page 1 of 43 • next >
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Answer: A: Circular dependencies between data and software packages: how best to avoid
... From bioc-devel, specifically Michael Lawrence and Valerie Obenchain (thanks to both of you! (Note that "SPB" refers to the Single Package Builder setup that allows for the scale of contributions that BioC receives, by decoupling what used to be a nightly mega-build.)  I imagine Lori is pretty busy ...
written 9 months ago by Tim Triche4.2k
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Circular dependencies between data and software packages: how best to avoid
... Hi all,    I came here to the support site prior to bothering bioc-devel, but searching for "circular dependencies" cf. https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages did not surface any answers that seemed relevant.  This seems like it might ...
bioc-devel developers package development circular dependencies written 9 months ago by Tim Triche4.2k • updated 9 months ago by shepherl ♦♦ 1.4k
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Comment: C: ChAMP Normalization on EPIC Methylation Data
... At the moment, functional normalization does not greatly enhance results over the underlying ssNoob performance on EPIC arrays (cf. https://academic.oup.com/bioinformatics/article/33/4/558/2666344 ). You might consider using straight noob, as funnorm's results will be dataset dependent, and ssNoob i ...
written 9 months ago by Tim Triche4.2k
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Comment: C: ExperimentHub wackiness (which breaks packages that depend upon experimentHub-pr
... sessionInfo() output breaks the 5000 character limit (of course...)  ```R R> sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)     Matrix products: default BLAS: /primary/vari/software/R/R-3.5.0/lib64/R/lib/libRblas.so LAPACK: ...
written 11 months ago by Tim Triche4.2k
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ExperimentHub wackiness (which breaks packages that depend upon experimentHub-provided *data pkgs)
... What does this mean? And why is it nearly impossible to get this to work? I have cleared the cache, taken various suggestions from ExperimentHub/BiocManager, and none of it helps. This... kind of sucks, to be honest. install("sesameData", localHub=TRUE) Bioconductor version 3.8 (BiocManager 1.30 ...
experimenthub written 11 months ago by Tim Triche4.2k • updated 11 months ago by Martin Morgan ♦♦ 23k
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Fast callback functions for scanTabix?
... This is one of those things I imagine *somebody* must have done, but I'm not finding an example of it.  In order to side-step compatibility issues between mac/windows/linux and also allow for reading of enormous (hundreds of millions to billions of loci from hundreds of subjects) files from (wait fo ...
tabix written 15 months ago by Tim Triche4.2k • updated 15 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Illumina MethylationEPIC vs. 450K
... You might also consult http://biorxiv.org/content/early/2016/07/23/065490 Since the results I have seen from Partek users sometimes suggests they are constrained by the software when analyzing methylation data. On the other hand, if you have a straightforward single platform experiment, that may ...
written 2.9 years ago by Tim Triche4.2k
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Comment: C: Removing sex-chromosome probes from methyLumiSet
... Hmmm, that's a featureFilter issue, but something I could fix... let me see if I can patch that and the methylumIDAT docs at the same time. Looks like I'll be writing a lot of patches today (i.e. the ones I wanted to write for ozymandias and DMRcate, and these) ...
written 4.1 years ago by Tim Triche4.2k • updated 4.1 years ago by Dan Tenenbaum8.2k
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Comment: C: Removing sex-chromosome probes from methyLumiSet
... 1) why would you want to toss out the X chromosome?  There are an awful lot of sites on chrX that matter 2) why not add a term for gender in the regression fit / DMRcate / whatever instead? 3) why not check that the sex of samples (from X copy number and/or X inactivation) matches the putative sex ...
written 4.1 years ago by Tim Triche4.2k
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Comment: C: Removing sex-chromosome probes from methyLumiSet
... 1) that's a GoldenGate example, there are no chrY probes on that platform 2) here is a vignette-length 450k example for methylumIDAT (which I should point to, now that you mention it, in the man page for methylumIDAT): http://www.bioconductor.org/packages/release/bioc/vignettes/methylumi/inst/doc/m ...
written 4.1 years ago by Tim Triche4.2k

Latest awards to Tim Triche

Popular Question 9 months ago, created a question with more than 1,000 views. For Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts
Popular Question 9 months ago, created a question with more than 1,000 views. For gmapR/gsnap crashes
Popular Question 11 months ago, created a question with more than 1,000 views. For gmapR/gsnap crashes
Popular Question 15 months ago, created a question with more than 1,000 views. For Interspecies differential expression of orthologs with Edger
Popular Question 15 months ago, created a question with more than 1,000 views. For Rsubread vs. BWA, Bowtie, etc. and RPKM vs. normalized counts
Popular Question 15 months ago, created a question with more than 1,000 views. For MethyLumiSet object
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Interspecies differential expression of orthologs with Edger
Popular Question 3.5 years ago, created a question with more than 1,000 views. For MethyLumiSet object
Popular Question 3.5 years ago, created a question with more than 1,000 views. For MethyLumiSet object
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: conceptual question about FDR, FDR adjusted p-value and q-value
Autobiographer 4.6 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.9 years ago, created 100 posts.

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