User: Bogdan

gravatar for Bogdan
Bogdan480
Reputation:
480
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Trusted
Location:
Palo Alto, CA, USA
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Last seen:
4 weeks, 1 day ago
Joined:
10 years, 5 months ago
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Posts by Bogdan

<prev • 251 results • page 1 of 26 • next >
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visualize CNV data based on WGS
... Dear all, we have been calling CNV (copy-number variations) in cancer genomes based on whole-genome sequencing data (WGS), using some of the packages available in BioC. Please would you advise -- what would be the best way to visualize WGS in order inspect visually the CNV predictions ? Is there ...
cnv written 4 weeks ago by Bogdan480
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
... Thank you. just found the answer : https://support.bioconductor.org/p/77193/ ...
written 10 weeks ago by Bogdan480
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
... Dear Aaron, great to hear from you, and thank you for suggestions. On a side note, thought I shall ask (following some old postings) : can we obtain the normalized counts by using also CPM function (below). Many thanks ! libSizes <- as.vector(colSums(x)) y <- DGEList(counts=x, group=grou ...
written 10 weeks ago by Bogdan480
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
... Dear Ryan, thank you for your reply. Here the question is not very much about TMM normalization (implemented in csaw or edgeR); I would be interested to know  whether I could normalize in the same procedure both ChIP samples and INPUT_DNA samples. Sorry if I missed the discussion in the manual. Any ...
written 10 weeks ago by Bogdan480
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normalization of CHIP-seq samples (ChIP and INPUT)
... Dear all, please could I have your advise on the following : shall we have multiple samples from ChIP experiments (where the proteins A, B, C were immuno-precipitated on the chromatin) and INPUT DNA (from the samples A, B, and C), would we normalize them all together (i.e. ChIP + INPUT) in edgeR, f ...
edger deseq2 voom limma written 10 weeks ago by Bogdan480 • updated 10 weeks ago by Aaron Lun18k
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Comment: C: normalization of ChIP-seq
... thank you Ryan. ...
written 11 weeks ago by Bogdan480
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normalization of ChIP-seq
... Dear all,  i would appreciate please a piece of advice please : what normalization method would you recommend in the following situation : someone did ChIP-seq experiments on protein X : 1) in cells that have the INTACT protein (control cells) and 2) in the cells where the protein X was KNOCKED- ...
limma edger deseq2 written 11 weeks ago by Bogdan480 • updated 11 weeks ago by Ryan C. Thompson6.3k
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extracting the exons coordinates on hg38
... Dear all, please could you advise : how can we obtain the coordinates of exons of the RefSeq or UCSC genes (canonical isoforms) on hg38, where each coordinates (chr, start, end) also have assigned the gene name .. ? thanks a lot, and a happy weekend, -- bogdan ...
genomefeatures written 4 months ago by Bogdan480
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Comment: C: about the runs with cn.mops
... Dear Gunter, thank you for your message and for confirmation. Yes, I thought that this may be the case, and we've used indeed the results from cnvs(). ...
written 5 months ago by Bogdan480
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Answer: A: about using the names of the rows and columns in ComplexHeatmap
... Continuing my previous email with an example : starting from the dataframe MAT and some annotations in DF/HA : library(ComplexHeatmap) library(circlize) set.seed(123) mat = cbind(rbind(matrix(rnorm(16, -1), 4), matrix(rnorm(32, 1), 8)), rbind(matrix(rnorm(24, 1), 4), matrix(rnorm(48, ...
written 5 months ago by Bogdan480

Latest awards to Bogdan

Popular Question 8 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 12 months ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 12 months ago, voted at least 25 times.
Centurion 2.0 years ago, created 100 posts.

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