User: Bogdan

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Bogdan520
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Palo Alto, CA, USA
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Posts by Bogdan

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Comment: C: gene set enrichment analysis
... Dear Gordon, thank you for your message. Yes, I have used a while ago the java implementation of GSEA that is available from Broad Institute, together with MSigDB database. Now, I am re-writing some RNA-seq analysis pipeline in R, and ideally, I would like to have all the analysis "chapters" in R, ...
written 10 days ago by Bogdan520
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gene set enrichment analysis
... Dear all, we wish you a fruitful autumn time ! I would like to ask  for a piece of advice, particularly, which R/BioC package would you recommend for GSEA (and it is close to java implementation available at http://software.broadinstitute.org/gsea/doc/desktop_tutorial.jsp ).  many thanks for your ...
gsea gsa written 10 days ago by Bogdan520 • updated 10 days ago by Gordon Smyth35k
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Comment: C: extracting gene names, gene id and transcript id
... During the last analysis, where 've mentioned the errors, the GTF files that 've used were from GENCODE: https://www.gencodegenes.org/releases/current.html ...
written 7 weeks ago by Bogdan520
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Comment: C: extracting gene names, gene id and transcript id
... Thank you Jaro. The links are : http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/ENSEMBL/homo_sapiens/ENSEMBL.homo_sapiens.release-83/ the file is : Homo_sapiens.GRCh38.83.gtf http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/GENCODE/GRCh38_Gen ...
written 7 weeks ago by Bogdan520
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Comment: C: the closest gene to a breakpoint
... Thank you Gordon. Happy to see that edgeR expands its set of functions ... ...
written 7 weeks ago by Bogdan520
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Comment: C: extracting gene names, gene id and transcript id
... thank you Jaro. I wish it works. On my Ubuntu system, by using a GTF file from STAR aligner website, it says : "terminate called after throwing an instance of 'std::length_error' what(): basic_string::_S_create Aborted (core dumped)" ...
written 7 weeks ago by Bogdan520
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extracting gene names, gene id and transcript id
... Dear all, given a GTF file (for example,  gencode.v28.basic.annotation.gtf), what is the simplest way to extract a table with the following information : -- gene_name -- gene_id -- transcript_id many thanks ! bogdan   ...
gtf written 7 weeks ago by Bogdan520 • updated 7 weeks ago by lee.s40
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Comment: C: the closest gene to a breakpoint
... Thank you Julie. I believe that I shall use the function " annoPeaks " ? ...
written 7 weeks ago by Bogdan520
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the closest gene to a breakpoint
... Dear all, please would you advise : given a list of chromosomes coordinates (i.e. BREAKPOINTS), and the list of genes promoters( i.e. TSS), how shall I get the closest gene TSS to a BREAKPOINT ? which function shall I use ? I am looking for a similar function as closestBed in bedtools  ... thanks ...
granges plyranges written 7 weeks ago by Bogdan520 • updated 7 weeks ago by Gordon Smyth35k
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sharing BiocWorkshops 2018
... Hi all, as I have seen this resource prepared by Sean Davis, thought to share it : https://bioconductor.github.io/BiocWorkshops/index.html   ...
rna-seq written 7 weeks ago by Bogdan520

Latest awards to Bogdan

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Voter 10 weeks ago, voted more than 100 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 15 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 15 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 16 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 20 months ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 20 months ago, voted at least 25 times.
Centurion 2.7 years ago, created 100 posts.

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