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I am curious about your thoughts on the best ATAC-Seq analysis strategy for differential accessibility analyses among experimental groups. We have data from a few related experiments totaling 8 condit…
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IN:04581274
Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield and fluorescence microscope images in order to detect tissue, align reads, generat…
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[Reopening Issue] Thanks for your quick reply! I am having trouble finding the 5' dataset on the 10X Genomics website. Is it no longer available? Can you share the link?
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"The input data…
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Hi,
I have 2 questions here:
1> I tried to use the function “train_cell_classifier” to train my classifier, but I have this error:
Error: is(object = cds, class2 = "CellDataSet") is not TRUE
It re…
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I have followed the ["getting started"](https://www.kallistobus.tools/getting_started) tutorial and generated the ```barcodes```, ```genes``` and ```mtx``` files. The ```gene.genes.txt``` file does no…
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Dear scruff team,
I have been trying to implement your tool for my analysis of a 10X library. I have been using the option to parallelize the demultiplexing. However, I ran into the problem that…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/lmweber/ggspavis
Confirm the following by editing…
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Hi everyone,
I hope to use DoubletFinder in my Seurat pipeline for scRNA-seq data from 3 donors of the same sorted cell population and cell type without any stimulation.
From various discussion…
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Hi,
I encountered Seurat package for single-cell RNA-Seq analysis. In addition to the tutorial, I am also interested in doing K-Means clustering on my 10X Genomics single-cell RNA seq data. I notic…
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**Describe the issue**
Firstly I just want to say I'm a huge fan of this tool and really appreciate how easy it is to run and the extremely clarity of the documentation. Decidedly one of the best too…