User: Nicolas Servant

gravatar for Nicolas Servant
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France
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Posts by Nicolas Servant

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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... Do you think you can fix it ? or is there any reason that explain the results ? Thanks ...
written 12 days ago by Nicolas Servant230
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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... I've got it. It is linked to the Granges object.   x1<- GRanges(c("chr1","chr2"), IRanges(c(1,10), c(100,1000)), score=c(12,15)) x2 <- GRanges(c("chr1","chr1"), IRanges(c(1,10), c(15,20)), score=c(12,15)) myTrackLine <- new("GraphTrackLine", type="bedGraph", name="test", description="tes ...
written 12 days ago by Nicolas Servant230
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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... I did, but it does not help. N > 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: /bioinfo/local/build/Centos/R/R-3.5.0/lib64/R/lib/libRblas.so LAPACK: /bioinfo/local/build/Centos/R/R-3.5.0/lib ...
written 12 days ago by Nicolas Servant230
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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... sure. Thanks R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 attached base packages: [1] parallel  sta ...
written 14 days ago by Nicolas Servant230
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rtracklayer export bedGraph cannot be loaded into UCSC
... Hi all, I have a simple question regarding the export function of rtracklayer. I have a GRanges object, and I would like to export a BedGraph file which can be loaded into the UCSC genome browser.   myTrackLine <- new("GraphTrackLine", type="bedGraph", name="mysample", description="mysample") ...
rtracklayer written 15 days ago by Nicolas Servant230 • updated 12 days ago by Michael Lawrence10k
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Comment: C: csaw normalization and library size
... Thanks for your feedback. Finally, I change a bit my code to use windowCounts on all genomic bins, and them removing bins overlapping peaks with the overlap function. That's way, I'm sure the lib.size is always based on the full genome information, with the same lib;size Thanks again   ...
written 7 weeks ago by Nicolas Servant230
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csaw normalization and library size
... Hi all, I have a short question about TMM normalization in csaw. I would like to normalize ChIP-seq histone marks data, and compare samples (WT vs KO). Before starting, I have my bam files, and results from peak calling. Here is my plan ; 1- Run bin counts over large genomic bins (10kb), where p ...
normalization chip-seq written 7 weeks ago by Nicolas Servant230 • updated 7 weeks ago by Aaron Lun21k
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Comment: C: visualize Hi-C .cool file in R
... In the HTCexp object, dimnames of the matrix (ie. colnames/rownames) should match the names of the GRanges object. I think it explains the error. N ...
written 9 weeks ago by Nicolas Servant230
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Comment: C: visualize Hi-C .cool file in R
... Hi, So far, there is no ready-to-use function to do import cool file into R (at least with HiTC). But it should be quite straighforward to write. You can have a look at the importC function as a template. Otherwise, I can do it for the next release. Best Nicolas ...
written 9 weeks ago by Nicolas Servant230
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Comment: C: Gene Density computation in pca.hic
... Hi Cath, Indeed, the gene density is calculated as  the number of genes falling in A (resp. B) compartments. Therefore as a sum. Would you have any reference explaining why using a mean might be better ? Best   ...
written 3 months ago by Nicolas Servant230

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