User: Bogdan

gravatar for Bogdan
Bogdan880
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880
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Palo Alto, CA, USA
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16 hours ago
Joined:
7 years, 4 months ago
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Posts by Bogdan

<prev • 249 results • page 1 of 25 • next >
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Comment: C: the analysis of multiple samples of 10X scRNA-seq
... thanks a lot for the very detailed suggestions ! ...
written 29 days ago by Bogdan880
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the analysis of multiple samples of 10X scRNA-seq
... Dear all, greetings i'd like to ask you for a piece of advise please : we have 3 scRNA-seq samples that were sequenced at different depths (200 mil reads, or 800 mil reads, 900 mil reads), and consequently, we do see : -- distinct numbers of cells, and -- (on average) distinct number of genes ...
scrna-seq scrnaseq written 29 days ago by Bogdan880 • updated 29 days ago by geek_y10.0k
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Comment: C: about batch correction in scRNA-seq
... thank you Shoujun, I am very glad that we can call Scanorama from R using the reticulate package (https://github.com/brianhie/scanorama) ...
written 5 weeks ago by Bogdan880
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about batch correction in scRNA-seq
... Dear all, referring to the batch correction methods for scRNA-seq, would you have any preference and/or comments ? among possible choices : -- MNNCorrect, as outlined in SimpleSingleCell workflows : https://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html -- ZINB-WAVE : ...
batch correction scrna scrnaseq written 5 weeks ago by Bogdan880 • updated 5 weeks ago by igor8.8k
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Comment: C: single cell RNA-seq pipeline
... and a few more slides : https://github.com/rhondabacher/ISMB2019_SingleCellTutorial ...
written 11 weeks ago by Bogdan880
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Comment: C: single cell RNA-seq pipeline
... thanks, another resource is : https://broadinstitute.github.io/2019_scWorkshop/scrna-seq-experimental-design.html ...
written 11 weeks ago by Bogdan880
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Comment: C: analysis of multiple batches and multiple treatment conditions in scRNA-seq
... thank you Sofia ... I m glad that the new Seurat pipelines address the question that we had. ...
written 3 months ago by Bogdan880
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analysis of multiple batches and multiple treatment conditions in scRNA-seq
... Dear all, please would you advise us on the following : for example, shall we have 2 batches of scRNA-seq data of 2 conditions (WT_batch1, WT_batch2, DISEASE_batch1, DISEASE_batch2), would the following approach be statistically legitimate in order to account/correct for the batch effect : **1 -- ...
scrna-seq deseq2 combat limma edger written 3 months ago by Bogdan880 • updated 3 months ago by sofiagreen7221130
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Comment: A: about the use of CellRanger aggr
... Dear Lior, on a side note, may I ask you please for another suggestion : what batch-correction method would you recommend for scRNA-seq ? CCA, MNNCORRECT, other methods ? thanks again ! ...
written 3 months ago by Bogdan880
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Comment: A: about the use of CellRanger aggr
... that is a great suggestion, thank you very much ! ...
written 3 months ago by Bogdan880

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Popular Question 13 days ago, created a question with more than 1,000 views. For filtering VCF files
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