User: Merienne Nicolas

Reputation:
120
Status:
Trusted
Location:
Switzerland
Last seen:
2 years ago
Joined:
5 years, 2 months ago
Email:
n***************@gmail.com

Posts by Merienne Nicolas

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Is there a way to align Hi-C half heatmaps to Gviz track?
... Hi Nicolas, Thank you for your answer. Indeed, the package HiTC seems to be interesting to generate this kind of plots. I will test it and see how the peaks look like (if I can interpret my data, it could be ok for me). Thanks. Nico ...
written 3.6 years ago by Merienne Nicolas120
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Comment: C: Is there a way to align Hi-C half heatmaps to Gviz track?
... Hi Robert, Actually, I did not try to do the heatmap with the DataTrack function. The data I am using are stored in an interaction matrix, in which each row/column represent a range of 40kb and each value represents the interaction intensity between the corresponding row and matrix. For example: ...
written 3.6 years ago by Merienne Nicolas120
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Is there a way to align Hi-C half heatmaps to Gviz track?
... Dear all, I am trying to handle Hi-C data to represent interactions between DNA segments. I got the data from the ENCODE publication of Shen et al 2012, Nature, in which, for each chromosome, interactions are represented as a file containing the matrix of interaction. Considering that each bin repr ...
gviz heatmap hi-c written 3.6 years ago by Merienne Nicolas120 • updated 3.6 years ago by Nicolas Servant260
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Comment: C: Gviz IdeogramTrack Hsapiens/Mmusculus error
... I updated rtracklayer and now it works for both hg19 and mm10. Thank you all for your help! Nico ...
written 4.4 years ago by Merienne Nicolas120
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Answer: A: Gviz IdeogramTrack Hsapiens/Mmusculus error
... I just used biocLite to reinstall rtracklayer and Gviz but I am still getting the same error... sessionInfo(): R version 3.2.0 Patched (2015-05-27 r68420) Platform: x86_64-apple-darwin10.8.0 (64-bit) Running under: OS X 10.6.8 (Snow Leopard) locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR ...
written 4.4 years ago by Merienne Nicolas120
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Comment: C: Gviz IdeogramTrack Hsapiens/Mmusculus error
... Indeed, this is working for hg19 but not for mm10 or older Mus muculus genome version... Is there something new for R 3.2.0? Thank you Nico ...
written 4.4 years ago by Merienne Nicolas120
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Comment: C: Gviz IdeogramTrack Hsapiens/Mmusculus error
... Hi Florian, Indeed, this fails for me too. Here is the error message : Error in unique(unlist(lapply(dots, methods:::.class1))) : erreur d'évaluation de l'argument 'x' lors de la sélection d'une méthode pour la fonction 'unique' : Error in unlist(lapply(dots, methods:::.class1)) : erreur d'év ...
written 4.5 years ago by Merienne Nicolas120
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Gviz IdeogramTrack Hsapiens/Mmusculus error
... Hello all, I have a strange error when trying to create an ideogram with Gviz IdeogramTrack function. Here is my code: library(Gviz) data(cpgIslands) chr = as.character(unique(seqnames(cpgIslands))) id = IdeogramTrack(genome = 'hg19', chromosome = chr) Error: too deeply nested evaluations: In ...
gviz written 4.5 years ago by Merienne Nicolas120
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Comment: C: mm10 ENSEMBL not available for GOSEQ
... Hello Nadia, I updated my R and goseq versions and it is working now without trying to retrieve informations from UCSC (and transcript lengths are the same as before). Thank you for your help! Best, Nicolas ...
written 4.5 years ago by Merienne Nicolas120
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Answer: A: mm10 ENSEMBL not available for GOSEQ
... Idomtamir, thank you for your comments. I also used another computer with a more recent R version with the same result... Anyway, I tried to manually construct my gene length vector but I am not sure to use the good tools. If I understand well, I have to correct for the length of transcripts (or th ...
written 4.5 years ago by Merienne Nicolas120

Latest awards to Merienne Nicolas

Great Question 3.3 years ago, created a question with more than 5,000 views. For Packages for GO and KEGG analysis on RNAseq data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For PCA for voom normalized RNAseq data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For mm10 ENSEMBL not available for GOSEQ
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Packages for GO and KEGG analysis on RNAseq data

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