User: Bogdan

gravatar for Bogdan
Bogdan470
Reputation:
470
Status:
Trusted
Location:
Palo Alto, CA, USA
Scholar ID:
Google Scholar Page
Last seen:
1 month, 2 weeks ago
Joined:
10 years, 2 months ago
Email:
t*****@gmail.com

Posts by Bogdan

<prev • 244 results • page 1 of 25 • next >
1
vote
0
answers
92
views
0
answers
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 6 weeks ago by Bogdan470
0
votes
2
answers
277
views
2
answers
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 9 weeks ago by Bogdan470
0
votes
1
answers
113
views
1
answers
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 9 weeks ago by Bogdan470
0
votes
1
answer
113
views
1
answer
about using the names of the rows and columns in ComplexHeatmap
... Dear all, after starting working with the package ComplexHeatmap, i would like to add a simple question (with my apologies if I missed the answer in the package documentation). The question is the following: shall we have numerical matrix/dataframe (with or without ROWNAMES or COLNAMES), is the O ...
complexheatmap written 9 weeks ago by Bogdan470
0
votes
0
answers
229
views
0
answers
Comment: C: an error on GRanges
... Dear Herve, as an solution for my question above, I am going to use the R code that you've suggested at :  https://support.bioconductor.org/p/100101/#100107 ; Many thanks again for your kind help !     ...
written 10 weeks ago by Bogdan470
0
votes
1
answers
237
views
1
answers
Comment: C: about setdiff() and meta-information in GRanges
... Dear Herve, many thanks for your help on this question. It is working very well now ;) ...
written 10 weeks ago by Bogdan470
0
votes
0
answers
229
views
0
answers
Comment: C: an error on GRanges
... Dear Herve, 'm happy to hear from you, and many thanks for time, help and suggestions. Will get back on this question, after a few more tests ;) ...
written 10 weeks ago by Bogdan470
3
votes
1
answer
237
views
1
answer
about setdiff() and meta-information in GRanges
... Dear all, please, could you advise, is there any way to keep the meta-information of a GRanges, during a setdiff() operation, with another GRanges. More precisely, shall we work with : > cnv_list GRanges object with 1081 ranges and 1 metadata column: seqnames ranges st ...
genomicranges granges written 11 weeks ago by Bogdan470 • updated 10 weeks ago by Hervé Pagès ♦♦ 13k
0
votes
0
answers
229
views
0
answers
an error on GRanges
... Dear all, I would appreciate your help on learning how to fix the following error ; thank you ! "Error: subscript is a NSBS object that is incompatible with the current subsetting operation" I am working with 2 Granges, let's call them "query" and "subject" (as shown below), and the purpose of the ...
granges written 11 weeks ago by Bogdan470
0
votes
2
answers
277
views
2
answers
Answer: A: about the runs with cn.mops
... Dear Gunter, please, it would be helpful, if I could have your insights on the following results. I have been running cnMOPS on TUMOR-GERMLINE sample, and for a particular case (on chr 11): -- cnvs() function gives the results (below), that contain a combination of CN1, CN3, and CN4 ...
written 11 weeks ago by Bogdan470

Latest awards to Bogdan

Popular Question 5 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 9 months ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 9 months ago, voted at least 25 times.
Centurion 21 months ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 149 users visited in the last hour