atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.

atarashansky/SAMap Issues

How SAMap deal with species-specific cell types/clusters in integration?
Updated 18 days ago
'coo_matrix' object has no attribute 'A'
Updated 19 days ago
dendrogram calculation issue
Updated 23 days ago
ImportError: cannot import name 'get_cmap' from 'matplotlib.cm'
Updated 2 months ago3
How to process the raw h5ad?
Updated 3 months ago
Bug to run the SAMap algorithm
Updated 3 months ago9
Export SAMap pairs results to Seurat
Updated 3 months ago
Best course of action when one has multiple datasets per species
Closed 4 months ago1
SAMap consistently generating a bifurcated UMAP
Closed 5 months ago7
Clustering in stitched space
Closed 6 months ago22
Gene filtering parameter
Closed 6 months ago3
Could alternative methods for BLAST be used?
Closed 7 months ago2
conda install: can't import samap
Updated 7 months ago1
Tagging Version
Updated 7 months ago
Reproducibility and seeding
Updated 4 months ago1
Combined umap for 1 cell lineage, retrieving latent representation
Updated 8 months ago
sankey and chord plot error
Updated 15 days ago12
installing issues
Updated 9 months ago
Harmony integration (was closed issue #83)
Closed 9 months ago6
how sankey_plot show more than four species
Updated 20 days ago7
sankey_plot error
Updated 9 months ago5
error in runing map_genes.sh
Updated 8 months ago1
Question about neigh_from_keys parameter
Updated 9 months ago1
"ValueError: could not convert string to float" in convert_eggnog_to_homologs()
Updated 7 months ago1
AttributeError after creating SAMAP object
Closed 10 months ago2
Mapping scores on edges
Updated 10 months ago
Cross-species UMAP scatter plots
Closed 2 months ago1
get_mapping_scores() for cell types within same species non-zero
Updated a year ago1
ModuleNotFoundError: No module named 'samalg'
Closed a year ago2
Multi-species cell type network plot
Updated 8 months ago1
Gene Pair Finder Giving "ValueError: negative dimensions are not allowed"
Updated a year ago1
UMAP looks like a line when neighborhood size was determined by using cell type labels
Updated a year ago5
The gene expression levels after SAMap-integrated are all greater than 0
Closed a year ago2
SAMap and Docker
Closed a year ago2
"ValueError: zero-size array to reduction operation" and other comments
Closed a year ago
How to use appropriate single cell data files as input files for SAMap correctly？
Closed a year ago1
SAMAP object instantiation fails with AttributeError
Updated a year ago1
Installation instructions in the README are wrong
Closed a year ago1
AttributeError: type object 'object' has no attribute 'dtype'
Closed a year ago5
Clarifying expression overlap plots
Closed a year ago2
Numba Dispatcher Issue with sm.run()
Updated 3 months ago14
the dtype of array is not correct
Updated a year ago
Neighbourhood graph or embedding?
Closed a year ago2
Running map_genes.sh
Closed a year ago2
transfer_annotations - removed
Closed a year ago8
Converting files
Closed a year ago2
"IndexError: boolean index did not match indexed array along dimension 0" in SAMAP call
Closed a year ago6
Do noe know which reference should be choosen for doing blast
Closed a year ago7
sankey_plot(MappingTable, align_thr=0.05, species_order = ['pl','sc','hy'])
Closed a year ago16
"Too many values to unpack" ENRICHMENT_SCORES,NUM_ENRICHED_GENES,ENRICHED_GENES = FE.calculate_enrichment(verbose=True)
Closed 2 years ago2