User: Bogdan

gravatar for Bogdan
Bogdan530
Reputation:
530
Status:
Trusted
Location:
Palo Alto, CA, USA
Scholar ID:
Google Scholar Page
Last seen:
18 hours ago
Joined:
11 years, 3 months ago
Email:
t*****@gmail.com

Posts by Bogdan

<prev • 293 results • page 1 of 30 • next >
0
votes
1
answers
46
views
1
answers
Comment: C: scRNA-seq: a question about the names of the columns in a Seurat object
... thanks a lot Steve ! that is very helpful and very informative ! ...
written 18 hours ago by Bogdan530
0
votes
1
answers
46
views
1
answers
Comment: C: scRNA-seq: a question about the names of the columns in a Seurat object
... Thank you Steve ! Yes, I am using both pipelines : 1) Seurat and 2) the workflow based on simpleSingleCell. Talking about batch effects, If I may add a question, as I have noted 2-3 strategies :  a. a strategy where the samples from multiple experiments are concatenated in a large matrix (as I hav ...
written 18 hours ago by Bogdan530 • updated 18 hours ago by Steve Lianoglou12k
0
votes
1
answer
46
views
1
answer
scRNA-seq: a question about the names of the columns in a Seurat object
... Dear all, please would you advise on the following : I am running the package Seurat on the dataset that was published in : https://www.ncbi.nlm.nih.gov/pubmed/27565351. https://github.com/broadinstitute/BipolarCell2016 In the article, there are 6 datasets on BIPOLAR cells that are all together ...
seurat scrna-seq written 23 hours ago by Bogdan530 • updated 19 hours ago by Steve Lianoglou12k
0
votes
1
answers
41
views
1
answers
Comment: C: getting the sequences of 3UTR and the gene names
... thank you James. great to hear from you ! ...
written 14 days ago by Bogdan530
0
votes
1
answer
41
views
1
answer
getting the sequences of 3UTR and the gene names
... Dear all,  please would you advise, what is the easiest way to get the SEQUENCES of 3'UTR and the GENE_NAMES for all mouse or human genes  ? After glancing through previous posts, I think I shall start with :  refSeq <- makeTxDbFromUCSC(genom="mm10",tablename="knownGene") ...
genomefeatures written 15 days ago by Bogdan530 • updated 15 days ago by James W. MacDonald48k
0
votes
0
answers
66
views
0
answers
Comment: C: normalization of ChIP-seq data
... Thank you Nicolas. Yes, we have used before edgeR for normalization at the level of promoter/TSS area, and it is great to have your suggestions on csaw and DiffBind.  Thanks ! ...
written 5 weeks ago by Bogdan530
0
votes
0
answers
66
views
0
answers
normalization of ChIP-seq data
... Dear all, please may I ask about your suggestions regarding the packages/methods that are available in R/BioC that I could use for ChIP-seq normalization (shall I compare two ChIP-seq datasets : before_treatment, and after_treatment). thanks a lot ! -- bogdan ...
normalization chip-seq written 5 weeks ago by Bogdan530
0
votes
1
answers
111
views
1
answers
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 9 weeks ago by Bogdan530
0
votes
1
answer
111
views
1
answer
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 9 weeks ago by Bogdan530 • updated 9 weeks ago by Gordon Smyth35k
0
votes
2
answers
263
views
2
answers
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 3 months ago by Bogdan530

Latest awards to Bogdan

Popular Question 9 weeks ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 9 weeks ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 12 weeks ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 12 weeks ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 12 weeks ago, created a question with more than 1,000 views. For about collapsed and expanded vcf file
Popular Question 3 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Voter 4 months ago, voted more than 100 times.
Popular Question 17 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 17 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 17 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 18 months ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 22 months ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 22 months ago, voted at least 25 times.
Centurion 2.8 years 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: 355 users visited in the last hour