User: Aliaksei Holik

gravatar for Aliaksei Holik
Reputation:
350
Status:
Trusted
Location:
Spain/Barcelona/Centre for Genomic Regulation
Twitter:
@AliakseiHolik
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Google Scholar Page
Last seen:
3 years, 5 months ago
Joined:
7 years, 7 months ago
Email:
s*******@bio.bsu.by

Posts by Aliaksei Holik

<prev • 40 results • page 1 of 4 • next >
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Comment: C: TxDb.Hsapiens.UCSC.hg19.knownGene Exons that are not part of any gene
... That's very clear. Thank you James and Hervé! ...
written 3.4 years ago by Aliaksei Holik350
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Comment: C: TxDb.Hsapiens.UCSC.hg19.knownGene Exons that are not part of any gene
... Thanks, fixed it. ...
written 3.5 years ago by Aliaksei Holik350
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TxDb.Hsapiens.UCSC.hg19.knownGene Exons that are not part of any gene
... Dear Bioconductors, This is a bit of a curiosity question. I have been working with TxDb.Hsapiens.UCSC.hg19.knownGene package and noticed that there are some exons, that do not seem to be a part of any gene. > # get all the genes > genic.regions <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene ...
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Comment: C: Efficiently finding a relative position inside a GRanges object
... It seems to be just what I needed. Thanks a lot! ...
written 3.6 years ago by Aliaksei Holik350
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Efficiently finding a relative position inside a GRanges object
... Dear BioConductors, I have two GRanges objects, one of which contains several sequences (let's say motifs) and the other is a single bp (let's say it's a variant): library(GenomicRanges) variant.position <- 63552595 variant.GR <- GRanges("chr17", IRanges(variant.position, width=1), "+") mot ...
genomicranges written 3.6 years ago by Aliaksei Holik350
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Comment: C: Can I feed TCGA normalized count data to EdgeR for differential gene expression
... That's a great resource, Stephen. Thanks! I do have a suggestion though. I wonder if it would be possible to use Entrez Gene IDs to annotate the count tables in future releases, rather than using Gene Symbols. After all, that's what Subread internal annotation is using. I suspect you might be using ...
written 4.0 years ago by Aliaksei Holik350
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Answer: A: Gviz: plotting mean values of biological replicates
... Hi Toomas. I've had the same problem with plotting ChIP-seq data. I got around it by using GenomicAlignments tools, which IMO gives you a bit more flexibility than purely relying on Gviz. The general workflow is: Read the region of interest from all the bam files -> Calculate the coverage over ...
written 4.0 years ago by Aliaksei Holik350
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Answer: A: Gene set analysis with CAMERA
... Presuming you have already done differential expression analysis with limma or edgeR, your design matrix and contrasts for the camera are the same. I would suggest checking out limma user guide: http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf Since you can' ...
written 4.8 years ago by Aliaksei Holik350
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Comment: C: "Normalising" GRanges coverage object
... That's great. Thanks Ryan! On 09/08/2014 04:40, Ryan wrote: > Hi Aliaksei, > > First of all, dividing by library size is not the way to go. It's wrong > in ChIP-seq for the same reason it's wrong in RNA-seq: compositional > bias. In order to properly normalize for sequencing depth, I ...
written 4.9 years ago by Aliaksei Holik350
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"Normalising" GRanges coverage object
... Dear Bioconductors and especially *Ranges team, I would like your expert opinion on whether what I'm doing is a sensible thing to do. I wish to plot some ChIP read coverage data in Gviz. The way I do it is by reading a number of bam files with readGAlignments() and calculating the coverage with th ...
coverage go gviz written 4.9 years ago by Aliaksei Holik350 • updated 4.9 years ago by Ryan C. Thompson7.3k

Latest awards to Aliaksei Holik

Popular Question 3.4 years ago, created a question with more than 1,000 views. For Gviz AnnotationTrack - Consistent y-scales
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Gviz AnnotationTrack - Consistent y-scales
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Gene set analysis with CAMERA
Scholar 4.8 years ago, created an answer that has been accepted. For A: Gene set analysis with CAMERA

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