Comments (8)
Hi @HelloWorldLTY, thanks for your interest in the dance
package! We are currently working on some heavy refactoring to clean up several interfaces, including datasets', and make them more user-friendly, e.g., apply methods to their own datasets, and benchmark their method on datasets provided by the package. As for now, there isn't an easy way to work with custom datasets. We expect to fix this within the next month or so.
Is your primary interest in using your custom dataset on joint-embedding tasks? If so, I can make that a priority so that you can play with the models soon.
from dance.
Thanks a lot, I am now working on JAE and since my dataset is very large, this tool is not very efficient.
from dance.
@HelloWorldLTY Currently, most datasets are loaded from an AnnData
object, which is one of the standard data objects for single-cell omics data. So long as your processed data structure can be interfaced with AnnData
easily, it shouldn't be a big deal.
Could you briefly describe the type of data structure you are working with and what libraries you currently use to process them? We can also consider adding interfaces for this particular type of data structure if it is somewhat standard as well.
from dance.
Hi, I prefer anndata object based on scanpy, and I am currently using this type of data.
from dance.
Ok, sounds good! This should be supported natively soon. I'll keep you posted on that.
from dance.
This is related to an ongoing refactoring task #49
from dance.
This is related to an ongoing refactoring task #49
yeah, I also get into trouble when I want to apply the jointembedding scmogcn model to my own GEX+ATAC data. My data is stored as annadata, and is there any tutorial that I can learn from?
from dance.
数据集在哪里下载
from dance.
Related Issues (20)
- Use the `download_unzip` utility in `ImputationDataset`
- Fix reported imputation metrics on readme for `GraphSCI` and `DeepImpute`
- Refactor multimodal dataset object to use the dance abstract dataset class
- Fix minor inconsistency at param init for CARD
- error about running dataset(openproblems_bmmc_cite_phase2 ) with scMoGCN HOT 1
- Where can I find documenation? HOT 1
- Running scmogcn.py example - fatal error HOT 1
- pip install pydance HOT 1
- Questions about conda installing HOT 1
- Feature: sanity checks
- Config support
- __init__.py missing from dance/metadata
- Random `segfault` when running pipeline tuning with `wandb` on certain machines
- Improve train/val/test data retrieval mech (instead of getting them individually?)
- Pipeline bypass mechanism to replace `*PlaceHolder` transforms
- Errors with Installation HOT 2
- Tutorial notebook is outdated HOT 1
- ImportError when directly running the code in the terminal HOT 1
- libcusparse.so.11 HOT 2
- Human PDAC (ST) for Spot Deconvolution is missing true_p.csv
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