User: Bogdan

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Bogdan690
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Posts by Bogdan

<prev • 230 results • page 1 of 23 • next >
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Comment: C: gene counts in Seurat after RunCCA() and AlignSubspace()
... Thank you, Igor. If I may add please a follow up question : for batch correction in scRNA-seq (when comparing multiple cell treatments), which algorithm would you recommend ? mnnCorrect() in SCRAN, combat() in SVA, or any other algorithm ? thanks a lot ! ...
written 5 days ago by Bogdan690
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Comment: C: gene counts in Seurat after RunCCA() and AlignSubspace()
... Thanks a lot, Avi. Yes, it is very helpful indeed. After extracting the NORM.DATA and SCALE.DATA for a few cells in the original matrix, and comparing the expression values at different steps in the algorithm : -- indeed I have not seen any changes in the numerical values in @DATA (there is no bat ...
written 5 days ago by Bogdan690
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Answer: A: gene counts in Seurat after RunCCA() and AlignSubspace()
... Thanks a lot, Avi. Yes, it is very helpful indeed. After extracting the NORM.DATA and SCALE.DATA for a few cells in the original matrix, and comparing the expression values at different steps in the algorithm : -- indeed I have not seen any changes in the numerical values in @DATA (there is no ba ...
written 5 days ago by Bogdan690
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Comment: C: gene counts in Seurat after RunCCA() and AlignSubspace()
... Thank you Igor .. oh well, as I am not a statistician, my thought was that AlignSubspace() function provides also "corrected" counts, as mnnCorrect() or Combat() would do. however, I can see that RunCCA() change the expression values in the @scale.data for some cells : if I may ask, how does it do ...
written 5 days ago by Bogdan690
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Comment: A: gene counts in Seurat after RunCCA() and AlignSubspace()
... In the continuation of my previous message, if I may rephrase the question above; I would appreciate having your insights :) After following the tutorial that is available at : https://satijalab.org/seurat/immune_alignment.html, the questions are : 1 -- after running *" immune.combined <- RunCC ...
written 6 days ago by Bogdan690
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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, and after I use RunCCA() and AlignSubspace(), as described here : https://satijalab.org/seurat/immune_alignment.html please would you let me kn ...
scrna-seq seurat cca written 16 days ago by Bogdan690
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Answer: A: scRNA-seq: a question about the names of the columns in a Seurat object
... thank you; 've received some advise on BioC website : https://support.bioconductor.org/p/116018/ ...
written 5 weeks ago by Bogdan690
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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 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 in a matri ...
scrna-seq written 5 weeks ago by Bogdan690
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Comment: C: annotation of SV (structural variants)
... Thanks a lot, Daniel ! yes, if you could please let us know when we can start using it, it would be very helpful ! ...
written 7 weeks ago by Bogdan690
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Comment: C: scRNA-seq, SEURAT, NormalizeData, ScaleData, PCA, CCA ...
... Hi Igor, thank you for your reply. If I may add a question please : is ScaleData() working on RAW_DATA or on NORMALIZED_DATA ? thank you ! ...
written 9 weeks ago by Bogdan690

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