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Run scanpy.pp.neighbors and UMAP on a different layer other than X?
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2
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440
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October 11, 2023
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Scanpy 1.10 release candidate
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0
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116
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February 23, 2024
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Error running veloVI when trying to add veloVI outputs to adata
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1
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531
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September 25, 2023
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scVI reproducibility seed issue
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2
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480
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September 7, 2023
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Model doesn't contain validation metrics
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7
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283
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October 12, 2023
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How to add metadata from csv file to concatenated anndata object?
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0
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700
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June 15, 2023
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Help concatenating var for cite seq
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2
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448
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May 24, 2023
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Interpretation of fold-changes in differential expression analysis
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2
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411
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May 17, 2023
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ImportError: cannot import name 'run_regression' from 'cell2location'
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2
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369
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March 26, 2024
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MERFISH data analysis from scratch
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2
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388
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June 4, 2023
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Not able to combine two samples for TCR analysis
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5
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305
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June 30, 2023
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Debugging Issue for CITE-seq analysis with totalVI juytper notebook tutorial
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6
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250
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June 21, 2023
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scGen generate irreproducible output
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6
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267
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July 24, 2023
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How to use lvm-DE
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3
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329
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June 2, 2023
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Reading in data with scanpy.read_10x_mtx gives back KeyError:1 when features.tsv contains only one column (gene symbols) and ValueError when adding 2 columns (gene ids and feature types)(
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0
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582
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May 17, 2023
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Error in Atlas-level-integration-of-lung-data Tutorial
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4
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264
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November 1, 2023
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Create SpatialData from Akoya Phenocycler qptiff
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5
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220
|
December 5, 2023
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Scvi-tools label transfer accuracy
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2
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357
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June 15, 2023
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How I can use big data with scanpy?
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1
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251
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July 3, 2023
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sq.pl.spatial_segment( TypeError: 'collection'
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1
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427
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May 24, 2023
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How to save intermediate checkpoints?
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3
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301
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February 3, 2024
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Re-integration after subseting cluster
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2
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328
|
September 26, 2023
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Save layer back to spatialdata from napari
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6
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208
|
November 15, 2023
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Is it possible to get the saved model from h5ad file?
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3
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267
|
October 17, 2023
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Cannot modify AnnData object
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2
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275
|
February 16, 2024
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How to properly save and load a TotalVI trained model that's based on mudata?
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1
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376
|
September 7, 2023
|
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CellAssign speed up
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2
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329
|
June 13, 2023
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Bar plot using muon between scRNA-seq and scTCR-seq&scBCR-seq?
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4
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259
|
July 6, 2023
|
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Computing sc.pp.neighbors without method?
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2
|
286
|
April 25, 2024
|
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Failure to remove a batch_key/ effect of number of LVs
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6
|
191
|
February 9, 2024
|
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How to show the cells on my umap projection based on barcodes
|
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2
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325
|
October 12, 2023
|
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scVI dropout, need for it?
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2
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153
|
January 10, 2024
|
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How to best integrate Genomic Variant Information
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1
|
200
|
August 16, 2023
|
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Questions about GimVI
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3
|
257
|
July 17, 2023
|
|
I am getting an error with sc.pp.neighbours()
|
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0
|
458
|
July 10, 2023
|
|
Need help with the napari.spatialdata Interactive() function
|
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3
|
254
|
August 7, 2023
|
|
Clustering with scVI latent space
|
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1
|
335
|
May 26, 2023
|
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Preserving biological variability in scVI sample integration
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4
|
252
|
February 16, 2024
|
|
Unexpected Coordinate Values with Image2DModel
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5
|
199
|
July 15, 2023
|
|
SCVI tools with large datasets
|
|
2
|
236
|
February 9, 2024
|
|
How to implement MonkeyBread pipeline for Visium spatial data
|
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4
|
229
|
August 22, 2023
|
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TypeError when trying to set up scvi.model.TOTALVI()
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2
|
270
|
August 29, 2023
|
|
Plotting spatialdata in only one coordinate system
|
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2
|
262
|
May 15, 2023
|
|
Gene shows up in dotplot, but it's not present in var_names
|
|
1
|
294
|
September 16, 2023
|
|
Sharing OBS between modalities
|
|
3
|
219
|
May 9, 2024
|
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Loading data into adata.obsm['airr'] of an existing scRNAseq object
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2
|
258
|
July 24, 2023
|
|
How to reorder adata according to sorted indices?
|
|
4
|
168
|
February 27, 2024
|
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Error in Fine-tuning scANVI Hyperparameters from Pretrained scVI Model
|
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2
|
223
|
November 20, 2023
|
|
Error with import scvi _
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|
1
|
319
|
October 10, 2023
|
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Struggling on under standing the parameter when clustering and cell type annotation. Also confused on normalization method
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0
|
411
|
June 6, 2023
|