User: gil.hornung

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gil.hornung70
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European Union
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1 year, 4 months ago
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4 years, 6 months ago
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Posts by gil.hornung

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Control probe sets in Affymetrix ST microarrays
... I also spent a lot of time trying to understand what are the different probe types and controls.Some of the answer can be found in the "Quality Assessment of Exon and Gene Arrays" whitepaper from Affymetrix. This is the current link: https://tools.thermofisher.com/content/sfs/brochures/exon_gene_a ...
written 2.3 years ago by gil.hornung70
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Comment: C: FASTA sequences of all human proteins, including variants
... Thanks Genomax, I hoped there is a file with all the sequences and not just the variation.... But I guess this will do. Gil ...
written 2.5 years ago by gil.hornung70
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FASTA sequences of all human proteins, including variants
... Hi all, I looking for a place where I can download the sequences of all known human proteins, including protein variants (for example variation caused by SNPs etc.) Thank you, Gil ...
protein sequences protein variation written 2.5 years ago by gil.hornung70
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"Similarity search" for epitopes
... Hi all, The problem I am facing is finding proteins that may react with antibodies that are produced against a specific protein (which I will refer to as protein X). I was thinking of collecting all proteins that are (roughly) similar to protein X using PSI-BLAST, and the predicting linear epitope ...
cross reactivity epitope prediction written 2.5 years ago by gil.hornung70
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Answer: A: Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (
... This is the answer I got from [Aaron Lun on bioconductor][1]: The multi-mapping reads (or lack thereof) should not affect how TMM normalization behaves. The assumption of TMM normalization on binned counts is that most regions of the genome are not marked, i.e., background, and all background regio ...
written 2.7 years ago by gil.hornung70
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Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
... Hi, I am interested in H3K9me2 signal (in S. Pombe), which is abundant on telomeres and centromeres. These regions are notorious for being highly repetitive. I clearly see an effect between treated and control samples in the coverage on telomeres, and I would like to quantify these differences usin ...
csaw chip-seq written 2.7 years ago by gil.hornung70
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Answer: A: 'How To' On Gene Ontology Analysis
... Regarding the first two items in you list, I just found the R library GO.db You can use the following functions: - `GOxxPARENTS`: the parents of the term - `GOxxANCESTOR`: the parents, and all their parents and so on. - `GOxxCHILDREN`: the children of the term - `GOxxOFFSPRING`: the children, ...
written 2.9 years ago by gil.hornung70
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Comment: C: How to get list of all GO terms in each ontology
... Great package! Saved me a lot of hassle ...
written 2.9 years ago by gil.hornung70
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Comment: C: "Shifted" copy number ratios coming from cnvkit?
... cpad0112, There is another support for that from the BubbleTree plots (generated using [this R package][1]). The x-axis presents the copy number ratio relative to the normal sample. The y-axis, HDS, is related to LOH events. It depicts the deviation from heterozygousity of SNPs in the tumor. So the ...
written 3.0 years ago by gil.hornung70
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Comment: C: "Shifted" copy number ratios coming from cnvkit?
... Thank you, Markus. ...
written 3.0 years ago by gil.hornung70

Latest awards to gil.hornung

Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to add a legend to the heatmap?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Somatic mutations from RNA-Seq data of tumor vs. normal
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Somatic mutations from RNA-Seq data of tumor vs. normal

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