Mo

I have a question about the conversion . I followed the tutorial (http://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/scvelo.html) and used example mouse bone marrow dataset. After converting seurat object to Anndata, I ran dynamical model....

Monocle 3 as.cell_data_set function for SCT assay

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I tried to Convert seurat object (SCT assay) to Monocle3 cell_data_set object, but it doesn't work `cds

Issue with expimap model

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`early_stopping_kwargs = { "early_stopping_metric": "val_unweighted_loss", # val_unweighted_loss "threshold": 0, "patience": 50, "reduce_lr": True, "lr_patience": 13, "lr_factor": 0.1, }` `intr_cvae.train( n_epochs=400, alpha_epoch_anneal=100, alpha=ALPHA, alpha_kl=0.5, weight_decay=0., early_stopping_kwargs=early_stopping_kwargs, use_early_stopping=True, monitor_only_val=False, seed=2024, )` `Preparing...

Velocity/pseudotime inconsistencies

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Hi, I worked on PBMC dataset (T Lymph, 950 genes after filtering). Based on stream plot of velocity, I can see the arrows point from naive T cell toward memory...

`query Scaling and synchronizing query gene expression Found 2295 out of 3000 reference variable genes in query dataset Project query cells using reference gene loadings Clustering query cells to reference...