User: Bogdan

gravatar for Bogdan
Bogdan550
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550
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Location:
Palo Alto, CA, USA
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Last seen:
3 months, 1 week ago
Joined:
11 years, 7 months ago
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Posts by Bogdan

<prev • 301 results • page 1 of 31 • next >
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Comment: C: about scRNA-seq, SEURAT and CCA
... Just in case that there is someone else asking the same question, 've found the answer here : "https://github.com/satijalab/seurat/issues/283", where the authors said an year ago that -- "Seurat does not return batch-corrected expression values (if we did, we would not be able to compare express ...
written 3 months ago by Bogdan550
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Comment: C: about scRNA-seq, SEURAT and CCA
... Hi James, we are so glad to hear from you, we wish you a happy and fruitful new year ! oh, well, i have not heard back from Seurat authors, and given the expertise of R/BioC users on scRNA-seq , I am hoping to have an answer (if you do not mind ..). thanks a lot ! ...
written 3 months ago by Bogdan550
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about scRNA-seq, SEURAT and CCA
... Dear all, I know that SEURAT is not a BioC package, and if I may have your permission to post the question here, hoping to have your insights ;) After following the tutorial that is available at : https://satijalab.org/seurat/immune_alignment.html, the questions would be : 1 -- after running *" ...
scrna-seq written 3 months ago by Bogdan550 • updated 3 months ago by James W. MacDonald49k
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gene counts in Seurat after RunCCA() and AlignSubspace()
... Dear all, happy and healthy new year ! I would appreciate your help on scRNA-seq analysis, as I am doing a comparison between 2 scRNA-seq datasets ; I am using SEURAT package and after I use RunCCA() and AlignSubspace(), as described here : https://satijalab.org/seurat/immune_alignment.html pleas ...
seurat scrna-seq cca written 3 months ago by Bogdan550 • updated 3 months ago by Aaron Lun23k
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Comment: C: about DropletUtils and scRNA-seq
... Dear Aaron, thank you very much. Having a workflow that will give a more detailed example on how to perform differential expression : 1) between conditions within each cluster, and 2) between conditions of different clusters, would be very very helpful. For our scRNA data analysis, we would like ...
written 3 months ago by Bogdan550
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Comment: C: about DropletUtils and scRNA-seq
... Thank you Aaron. If I may add a question about scRNA-seq analysis (of 10X_Genomics datasets) : we have 3 experimental conditions to compare (i.e. 3 scRNA-seq datasets : control, treatment1, treatment2). when I analyze each dataset, i could apply the pipelines that you comprehensively described at ...
written 3 months ago by Bogdan550
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Comment: C: about DropletUtils and scRNA-seq
... ... just found the function in the tutorial together with the explanations of the Monte Carlo procedure and the choice of FDR < 0.01 (sorry, 've overlooked it ..) sce <- sce[,which(e.out$FDR <= 0.01)] ...
written 3 months ago by Bogdan550
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about DropletUtils and scRNA-seq
... Dear Aaron, and all, happy and healthy new year ! I was following the tutorial presented at : https://master.bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/work-3-tenx.html may I ask, what function do you use in order to remove from a SCE object the barcodes with ...
dropseq dropletutils droplet written 3 months ago by Bogdan550 • updated 3 months ago by Aaron Lun23k
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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 4 months ago by Bogdan550
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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 4 months ago by Bogdan550 • updated 4 months ago by Steve Lianoglou12k

Latest awards to Bogdan

Popular Question 4 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 6 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 6 months ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 7 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 7 months ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 7 months ago, created a question with more than 1,000 views. For about collapsed and expanded vcf file
Popular Question 7 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
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Popular Question 22 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 Fwd: edgeR dispersions
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For gene symbols in Gviz
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Centurion 3.2 years ago, created 100 posts.

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