User: Bogdan

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Bogdan490
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Palo Alto, CA, USA
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5 days, 11 hours ago
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10 years, 11 months ago
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Posts by Bogdan

<prev • 270 results • page 1 of 27 • next >
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display of synteny regions across multiple species
... Dear all,  I am looking for  R packages that display the synteny regions across multiple species (here please see an example Figure 1 from http://www.g3journal.org/content/7/6/1775.figures-only ) in the context of a previous post I had on chromosomal translocations (https://support.bioconductor.org ...
evolution synteny translocation conservation written 22 days ago by Bogdan490
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Comment: C: display of chromosomes (on the linear scale) and translocations
... On the same line of thought,  I believe that I could adapt the functionality of some R packages that display the synteny regions across multiple species (here please see an example Figure 1 from http://www.g3journal.org/content/7/6/1775.figures-only ), In my case, instead of distinct species, I wil ...
written 22 days ago by Bogdan490
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display of chromosomes (on the linear scale) and translocations
... Dear all, please would you advise if there is any package in BioC/R that could help with the following data visualization :  1 -- we have a set of SNV, CNV, SV from cancer samples 2 -- we would like to display the SNV and CNV along the chromosomes (on the linear scale, ie. HORIZONTALLY) 3 -- we ...
gviz ggplot2 rcircos circlize ggviz written 23 days ago by Bogdan490
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Comment: C: single cell RNA-seq pipeline
... You gentlemen are awesome ! Aaron and Martin, thank you very much ! ...
written 4 weeks ago by Bogdan490
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single cell RNA-seq pipeline
... Dear all, please would you advise about a single cell RNA-seq pipeline/scRNA-seq libraries in R/BioC that are both mature and user-friendly that we can use ? Thank you very much,    bogdan   ...
rnaseq scrna-seq written 4 weeks ago by Bogdan490 • updated 4 weeks ago by Aaron Lun20k
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Comment: C: visualization of chromatin interaction networks
... Thanks a lot, Aaron, for your reply : it is always great to hear from you. Yes, I've embraced so far the same strategy, i.e. to use the package "igraph" (http://kateto.net/network-visualization), although I am also looking into : tidygraph : https://github.com/thomasp85/tidygraph ggraph : https:// ...
written 6 weeks ago by Bogdan490
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visualization of chromatin interaction networks
... Dear all, please would you advise if there is any tool in BioC that could help with  the visualization of CHROMATIN INTERACTION NETWORKS as a GRAPH (where NODES="chromosome loci", and EDGES = "interactions").  Thanks a lot ! -- bogdan   ...
ggbio gviz karyotyper written 6 weeks ago by Bogdan490 • updated 6 weeks ago by Aaron Lun20k
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Comment: C: an error in BioMart regarding gene annotations
... Thank you Daniel, and Martin, for your help, time, suggestions and explanations. I may work then with : transcripts(TxDb.Hsapiens.UCSC.hg38.knownGene) instead of genes(TxDb.Hsapiens.UCSC.hg38.knownGene).   ...
written 6 weeks ago by Bogdan490
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Comment: C: an error in BioMart regarding gene annotations
... Thank you Mike. Yes, I share the same opinions. For now, I will just ignore those genes, until a new release of  "org.Hs.eg.db" becomes available. Thank you. ...
written 6 weeks ago by Bogdan490
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Comment: C: an error in BioMart regarding gene annotations
... Dear Martin, thank you for your suggestion. To me ... hmmm ... it is still a bit surprising: for example, shall I input the coordinate ("chr21:21004327-21004328") that overlap NCAM2 gene, the result (after running your code) is the following (below). It contains NCAM2 gene, but also those additional ...
written 6 weeks ago by Bogdan490

Latest awards to Bogdan

Popular Question 13 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 13 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 13 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 14 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 18 months ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 18 months ago, voted at least 25 times.
Centurion 2.5 years ago, created 100 posts.

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