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Hi,
I am particularly interested in the scATAC-seq data you generated as part of your study. To further my research, I would like to request access to the metadata information (such as cell type a…
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Testing for differential expression/accessibility is embarrassingly parallel, and could use all available cores by default.
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scATAC-seq BAM files from CellRanger can be used with VarCA, but there is an important caveat that one should be aware of:
**tldr; if you give VarCA BAM files, you must provide the exact same refer…
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Hi @rcorces
I tried to integration scRNA and scATAC, but I get the following error:
- seuratRNA_2
An object of class Seurat
31053 features across 7264 samples within 1 assay
Active assay: …
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Hello,
How do you decide on `n_sample_cells` & `n_sample_peaks` in the Mouse pancreatic endocrinogenesis (scATAC-seq) Tutorial?
Do you have any benchmarks?
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Hi, I'm trying to run the function runGenePeakcorr with the sparse matrix for scRNAseq and SummarizedExperiment object of scATACseq and get this error:
Error in if (!class(obj) %in% c("SummarizedEx…
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Hi all,
I'm testing `chromap` and I'd say I'm impressed by the performances. In addition to the current options, would you consider the possibility to output counts over given intervals? Catalogs of…
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Hi Alex,
I am running STAR on the same paired-end data as described in [issue #558](https://github.com/alexdobin/STAR/issues/558). Thank you again for allowing paired end mapping for scATAC-seq dat…
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I have reviewed the tutorial to integrate scRNA-seq and scATAC-seq data (https://satijalab.org/seurat/articles/seurat5_atacseq_integration_vignette). If I have multiple conditions, do I integrate all …
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Depends on proper barcode information in fastq file names.
https://github.com/nathankw/pulsar_lims/issues/90