Yiming Yang
Yiming Yang
Hello, I'm wondering if there is a way to specify the `zones` in Cromwell's configuration file that overwrites all the jobs executed through the Cromwell server running it. When checking...
Hello, Cromwell has runtime attributes such as `gpuCount`, `gpuType` and `nvidiaDriverVersion` (https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/#gpucount-gputype-and-nvidiadriverversion), but it seems they only work for GCP. So I'm wondering if AGC, [genomics workflows](https://github.com/aws-samples/aws-genomics-workflows), or [Cromwell-AWS](https://github.com/henriqueribeiro/cromwell) provides...
## Usage In `sccoda.util.comp_ana.CompositionalAnalysis`, add `seed` optional parameter: * If not specifying a value, it behaves as normal. * If specifying a value as the following: ``` from sccoda.util import...
When compiling with GHC 8.4.3, a liberal coverage condition failure happened for "HasValue" typeclass instance declarations in "Imperative/Internals.hs", Line 86 and 88. For the functional dependency "b -> r i",...
* In `violin`, `heatmap`, `scatter`, `dotplot`, `scatter_matrix`, `embedding`, `variable_feature_plot`, `volcano`, `composition_plot`, make `adata` be of either `AnnData` or PegasusIO `MultimodalData` type. And in code, if `adata` is not `AnnData`, convert...
**Describe the bug** My following code ```python from pydeseq2.dds import DeseqDataSet from pydeseq2.default_inference import DefaultInference inference = DefaultInference(n_cpus=1) dds = DeseqDataSet(counts=..., metadata=..., design_factors=..., inference=inference, quiet=True) dds.deseq2() ``` still prints the...
Hello, First, thank you for developing such a great tool! When trying your package on our CosMx data, I found that its runtime and memory usage performance seem down-perform comparing...
Hello, Thanks for developing this great tool! When reading through [your paper](https://www.biorxiv.org/content/10.1101/2024.04.25.591218v1), in Figure 9, I see that you used the degree of spurious coexpression as one of the metrics...
Hello, I'm working on making our cromwell server work with GCP Batch and running in our private VPC network. However, after following [this tutorial](https://cromwell.readthedocs.io/en/develop/backends/GCPBatch/), I encounter the following error: ```...
Hello, I was trying Proseg v1.1.3 on our Xenium 5k dataset, which has 301,710,014 transcripts, 573,137 cells estimated initially, and 10,029 genes, and with 16 threads (my machine has 32...