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Hi,
I am using Tangram to align scRNA-Seq reference onto spatial data. My scRNA-Seq reference is a collection of samples from different datasets. As a result, the raw gene expression of the scRNA-S…
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Hi,
Sorry for this issue but I didn't arrive to lauch mersim :
1. I clone this project and the MERlin one
2. I define the PARAMETERS_HOME as the path to examples/merfish-parameters
3. I moved to …
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Hi Anna and David,
I am interested to apply ncem for one of the MERFISH data. But I do not understand how to make dataloader for this data.
It would be very grateful if you can help me to bui…
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Hi, I am interested in using Tangram for my data.
We have multiple types of spatial transcriptome data(Visium/merFISH...) and single-cell data(10X/smart-seq), so we hope to run different data pairs…
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Researchers need to be aware of which data are single-cell vs single-nucleus so that they can take special care to ensure proper integration.
Most contributors don't provide it automatically because …
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There are some general, common plots we could quickly put behind a `dodola validate ...` command (for example).
This might be worth a new module or breaking `dodola.core` into submodules.
We'd …
brews updated
3 years ago
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Make a module for loading formatted datasets.
Data loading strategy
- check for data locally
- download from figshare if doesn't exist
See seaborn for reference: https://github.com/mwaskom/sea…
ckmah updated
3 years ago
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**Snakemake version**
6.1.0
**Describe the bug**
In some situations, putting ancient() around input files causes rules to be run before the input files they need exist.
**Minimal example**
H…
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The Description for [Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics](https://cellxgene.cziscience.com/collections/9132fa…
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Hi, we are seeing unexpected UMAP embeddings using the 0.5.2 umap-learn version, run via Scanpy, with our single cell gene expression data ([publicly available MERFISH data from Vizgen](https://vizgen…