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Hello, I experienced some very strange with the `cgdsr` backend, because profile ‘brca_metabric_mrna_U133_Zscores’ disappeared for study ‘brca_metabric’, case ‘brca_metabric_all’, which I was able to …
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The parameters of the transform function are
```
def transform(self, X, perplexity=5, initialization="median", k=25,
learning_rate=100, n_iter=100, exaggeration=2, momentum=0, max_grad_norm=0.05)…
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How does MAGIC take into account the fact that most of the density of a high-dimensional volume is concentrated on the surface? Let's say that for log-transformed sc-RNA-seq data, you have a ~20.000 d…
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For the first public release of our pipeline, we should make it independent using docker and conda.. Then we can also see whether we can add some some travis tests (issue #34) .
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we have some scRNA-seq data from C1 system. Mapping plot shows it's a kind of 3' end RNA seq.
how to process these data, i couldn't quit know these info even after reading your paper and readme on …
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Hi Pavlin! Great work. I did not know about Orange but I am working with scRNA-seq data myself (cf. your Zeisel2018 example) and I am using Python, so it's interesting to see developments in that dire…
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The following results in an error using **scPipe** v1.3.7:
```R
sce = create_sce_by_dir(data_dir, pheno_data = DataFrame(row.names = colnames(sce)))
#> Error: subscript contains invalid namesErro…
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I have seen two PAGA plots for the 1.3mln 10x dataset: Figure S12 in https://rawgit.com/falexwolf/paga_paper/master/paga.pdf and slide 17 in http://falexwolf.de/talks/180313_HCA_RedBox_Scanpy.pdf. The…
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Thanks for putting together and maintaining this list, it's a great community resource!
I noticed that SCRAT is listed in the RNA-seq section when it's really ATAC-seq...or epigenomics in general. …
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To date there is no way to distinguish scRNA-Seq data from RNA-Seq data since there is no real library prep platform to distinguish them, nor is there a distinct assay or data type. Should we add one?…