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### Description of feature
# Description
https://qupath.github.io/
https://www.10xgenomics.com/support/software/xenium-explorer/latest/tutorials/xe-image-file-conversion
Can we implement this?
heylf updated
2 months ago
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Multiple sets of MEX files can be aggregated into a single file triplet.
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/aggr-outputs
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### Description of feature
Repo
https://github.com/kharchenkolab/Baysor
Description of feature
https://www.10xgenomics.com/analysis-guides/using-baysor-to-perform-xenium-cell-segmentation
I…
heylf updated
2 months ago
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### Name of the tool
cellranger multi
### Tool homepage
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
### Tool description
is a…
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Hello! I have installed the tool and called it (it states that there are 32 warnings) However, it seems to be loaded just fine. when I run it on the sample, the first part is done and the .rds file is…
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# Changelog
* uns (Dataset Metadata)
* Updated the requirements for `spatial` to include descendants of _Visium Spatial Gene Expression_.
* Updated the requirements for spatial['is_single']…
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Hello,
I heard that Meringue was used to compute the correlation between genes in the Visium 10XGenomics public datasets posted on their website (https://www.10xgenomics.com/resources/datasets). Is…
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Hi,
in your tutorial notebook, you use
`fns_covar = ["vdj_v1_hs_aggregated_donor1_binarized_matrix_extended_covariates.csv",
"vdj_v1_hs_aggregated_donor2_binarized_matrix_extended_co…
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Hello!
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I have a 10xgenomics pipeline generated bam file. And I am getting this error when I use your tool. I have also tried marking and removing the duplicate reads, but to no avail. Could you p…
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It appears that in the cell ranger code, the dispersion is calculated using the negative binomial relationship between mean and dispersion, see
https://github.com/10XGenomics/cellranger/blob/5f5a62…