atarashansky SAMap issues

atarashansky / SAMap

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

MIT License

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issues

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Adapting GenePairFinder to identify gene pairs with divergent expression in a pair of clusters?

#154 laracbusby opened 1 month ago
0
ValueError: zero-size array to reduction operation

#153 laracbusby closed 1 month ago
0
problem in intetpreting the SAMap integration results

#152 GGboy-Zzz opened 2 months ago
2
How SAMap deal with species-specific cell types/clusters in integration?

#151 DiracZhu1998 opened 4 months ago
0
'coo_matrix' object has no attribute 'A'

#150 dnjst opened 4 months ago
0
dendrogram calculation issue

#149 DiracZhu1998 opened 4 months ago
0
ImportError: cannot import name 'get_cmap' from 'matplotlib.cm'

#148 kelsell15 opened 6 months ago
3
Update setup.py

#147 atarashansky closed 7 months ago
0
How to process the raw h5ad?

#146 jordan841220 opened 7 months ago
3
Bug to run the SAMap algorithm

#145 xiangyuma1995 opened 7 months ago
9
Export SAMap pairs results to Seurat

#144 silvainp opened 7 months ago
0
Best course of action when one has multiple datasets per species

#143 matejasoretic closed 8 months ago
1
SAMap consistently generating a bifurcated UMAP

#142 dariotommasini closed 9 months ago
7
Clustering in stitched space

#141 dariotommasini closed 10 months ago
22
fix: incorrect _smart_expand parameter

#140 atarashansky closed 10 months ago
0
Gene filtering parameter

#139 dariotommasini closed 10 months ago
3
Could alternative methods for BLAST be used?

#138 Budjavac closed 10 months ago
2
conda install: can't import samap

#137 jowodo opened 11 months ago
1
Tagging Version

#136 jowodo opened 11 months ago
0
Reproducibility and seeding

#135 dariotommasini opened 11 months ago
1
Combined umap for 1 cell lineage, retrieving latent representation

#134 nhgopee opened 1 year ago
0
sankey and chord plot error

#133 dsb66 opened 1 year ago
12
installing issues

#132 stevenjblair opened 1 year ago
0
Harmony integration (was closed issue #83)

#131 dsb66 closed 1 year ago
9
how sankey_plot show more than four species

#130 xmChen090 opened 1 year ago
7
Update analysis.py

#129 zEpoch closed 10 months ago
0
sankey_plot error

#128 zEpoch opened 1 year ago
5
error in runing map_genes.sh

#127 rdf1993 opened 1 year ago
1
Question about neigh_from_keys parameter

#126 Bassi-git opened 1 year ago
1
"ValueError: could not convert string to float" in convert_eggnog_to_homologs()

#125 Zaffe24 opened 1 year ago
1
AttributeError after creating SAMAP object

#124 colinshew closed 1 year ago
2
Mapping scores on edges

#123 DinithiRajapaksha opened 1 year ago
0
Cross-species UMAP scatter plots

#122 zhongzheng1999 closed 6 months ago
1
get_mapping_scores() for cell types within same species non-zero

#121 dnjst opened 1 year ago
1
ModuleNotFoundError: No module named 'samalg'

#120 DinithiRajapaksha closed 1 year ago
2
Multi-species cell type network plot

#119 dnjst opened 1 year ago
1
Gene Pair Finder Giving "ValueError: negative dimensions are not allowed"

#118 acgarretson opened 1 year ago
2
UMAP looks like a line when neighborhood size was determined by using cell type labels

#117 Evenlyeven opened 1 year ago
5
The gene expression levels after SAMap-integrated are all greater than 0

#116 HYJ-hh closed 1 year ago
2
SAMap and Docker

#115 avianalter closed 1 year ago
2
"ValueError: zero-size array to reduction operation" and other comments

#114 avianalter closed 1 year ago
0
How to use appropriate single cell data files as input files for SAMap correctly？

#113 HYJ-hh closed 1 year ago
1
SAMAP object instantiation fails with AttributeError

#112 carlosj-rr opened 1 year ago
1
Installation instructions in the README are wrong

#111 pnewstein closed 1 year ago
1
AttributeError: type object 'object' has no attribute 'dtype'

#110 yangqi1999 closed 1 year ago
5
Clarifying expression overlap plots

#109 dkeitley closed 1 year ago
2
Numba Dispatcher Issue with sm.run()

#108 mikepassal opened 1 year ago
14
the dtype of array is not correct

#107 wubaosheng opened 1 year ago
0
Neighbourhood graph or embedding?

#106 YY-SONG0718 closed 1 year ago
2
Running map_genes.sh

#105 wershofe closed 1 year ago
2