User: Tiphaine Martin

Reputation:
40
Status:
New User
Location:
France
Last seen:
4 months, 1 week ago
Joined:
4 years, 4 months ago
Email:
t**************@kcl.ac.uk

Posts by Tiphaine Martin

<prev • 31 results • page 1 of 4 • next >
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Answer: A: "> example(coMET)" returns error in genesENSEMBL() call
... Hi, Sorry, I forgot to update this section too.As you see in the manual  genesENSEMBL has been replaced by genes_ENSEMBL. So please, use genes_ENSEMBL and not genesENSEMBL. I will update the manual.   Best, Tiphaine    ...
written 4 months ago by Tiphaine Martin40
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News: Quantitative Genomics 2018 - Thursday 14th of June 2018 at University College London
... ---- Quantitative Genomics London 2018    Quantitative Genomics 2018  Thursday 14 June 2018  University College London (UCL)   We are excited to announce  Quantitative Genomics 2018 (QG18) , a conference for early-career researchers  in quantitative genomics that will take place on  Thursday 1 ...
news conference written 4 months ago by Tiphaine Martin40
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Comment: C: getBM in loop
... I made the request of more than 20,000 genes per tissue and run this request for several tissues. sorry this remark was not very clear. I don't make a loop for each genes but by tissue. Some of these request fail. I asked to rerun and for the tissue failling and for the following tissues, manually, ...
written 6 months ago by Tiphaine Martin40
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getBM in loop
... Hi, Could you advise me how to run "getBM" in a loop when the connection is too long and ask to rerun until I have a results ? I see that there is a option called curl, but I never used. So I don't know how to use it.   library(biomaRt) #connexion to ENSEMBL mart <- useMart(biomart = "ENSE ...
biomart ensembl curl written 6 months ago by Tiphaine Martin40 • updated 6 months ago by Mike Smith2.8k
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Answer: A: Gviz ChromHMM colouring for AnnotationTracks
... Hi, In my r package coMET, I allow user to visualise chrommHMM using Roadmap color or our color https://bioconductor.org/packages/release/bioc/html/coMET.html, you have different color sets described in the vignette.  This was implemented in the function "chromHMM_RoadMap". Feel free to use it and ...
written 7 months ago by Tiphaine Martin40
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Answer: A: Gviz - UcscTrack
... Hi, This error and related to the link between Gviz and UCSC When I apply with this general features (it better that you give us your area that you want to visualize) gen <- "hg19"  chr <- "chr2"  start <- 38290160 end <- 38303219 I have another error message : Error in UcscTrack(ge ...
written 7 months ago by Tiphaine Martin40
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Answer: A: ENCODE examples from vignette do not work (missing data?)
... Hi, Sorry for the delay to answer. The new version of coMET have the file ENCODE data directory. Regards, tiphaine ...
written 7 months ago by Tiphaine Martin40
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Comment: C: ENCODE examples from vignette do not work (missing data?)
... Hi,   Sorry for the delay to answer. The new version of coMET have the file ENCODE data directory. Regards, tiphaine ...
written 7 months ago by Tiphaine Martin40
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Comment: C: install new package from bioconductor
... http work, but not https for me. Thank you. ...
written 2.7 years ago by Tiphaine Martin40
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Answer: A: install new package from bioconductor
... Hi Julie,   It works, but why is  in the page of S4Vector, the instruction to install this page ? source("https://bioconductor.org/biocLite.R") biocLite("S4Vectors") I checked for my package and I have what you propose. any way, it works. So I can carry on :) Thanks, Tiphaine ...
written 2.7 years ago by Tiphaine Martin40

Latest awards to Tiphaine Martin

Popular Question 2.2 years ago, created a question with more than 1,000 views. For use BiomartGeneRegionTrack with the dataset grch37.ensembl.org
Popular Question 2.2 years ago, created a question with more than 1,000 views. For installation of GenomicRanges package in Rdevel fails
Popular Question 2.2 years ago, created a question with more than 1,000 views. For install new package from bioconductor
Scholar 2.7 years ago, created an answer that has been accepted. For A: install new package from bioconductor
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Issue to install biomaRt, Gviz, rtracklayer, and S4Vectors under BioC 3.0

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