User: rosano

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rosano0
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Posts by rosano

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Comment: C: Running DropletUtils::swappedDrops() on multiplexed samples from different libra
... Thank you for the fast reply. Regarding the choice of analysis setting: since the last CellRanger update it is now possible to process ADT libraries independently from GEX, and this is what we do in our pipeline since it shows higher quality in results when comparing to the combined GEX and ADT anal ...
written 20 days ago by rosano0
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Running DropletUtils::swappedDrops() on multiplexed samples from different libraries
... Hi all, To give you some context: We have an experimental setting with 2 samples, where GEX (gene expression) and ADT (antibody labelling) libraries are generated from the same sample. So, in total, 4 samples are generated corresponding to 2 pairs of paired GEX-ADT samples. Specifically following ...
dropletutils swappeddrops written 4 weeks ago by rosano0 • updated 29 days ago by Aaron Lun25k
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Comment: C: Scalability of emptyDrops() running times
... Thank you very much for your detailed response, and apologies about the very very late reply... I was delaying this answer until having some feedback on usage of this `BPPARAM` parameter, however, in the end I have not had the time yet to test and play around with it. Nonetheless, I plan to do so in ...
written 5 months ago by rosano0
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Comment: C: Recommendations for running DropletUtils::swappedDrops() on multiplexed samples
... Thank you very much for your answers and for detailing the experiment setup once more. We do not intend to mix extra samples into the multiplexing, but will always chose a setup as you describe here: > Now, the simplest case in which swappedDrops will work is: - 5' libraries for samples A-F are ...
written 7 months ago by rosano0
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Scalability of emptyDrops() running times
... Hi all, Currently I am using emptyDrops() for calling cells after applying swappedDrops() to perform barcode swapping removal of several 10X scRNA datasets. After experiencing long running times for emptyDrops() on these data, I was wondering about the scalability of the function's performance. A ...
dropletutils emptydrops written 7 months ago by rosano0 • updated 6 months ago by Aaron Lun25k
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Comment: C: Recommendations for running DropletUtils::swappedDrops() on multiplexed samples
... Dear both, Thank you very much for your quick reply and for the detailed explanations! So, as long as we avoid an intermixing of samples for the multiplexing (between libraries, as described in your alternative scheme with 6 mixed samples), swappedDrops should be able to correctly compare the sampl ...
written 7 months ago by rosano0
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Recommendations for running DropletUtils::swappedDrops() on multiplexed samples from multiple libraries
... Hi all, Regarding the following passage from the description of swappedDrops() from package DropletUtils: *“In files produced by CellRanger version 3.0, an additional per-molecule field is present indicating the (c)DNA library from which the molecule was derived. Library preparation can be perform ...
dropletutils swappeddrops written 7 months ago by rosano0 • updated 7 months ago by Aaron Lun25k

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