atarashansky self-assembling-manifold issues

atarashansky / self-assembling-manifold

The Self-Assembling-Manifold (SAM) algorithm.

MIT License

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issues

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haromy using scanpy external.sam

#47 Marwansha closed 3 weeks ago
0
Division by zero warning during sum_norm

#46 georgyFenix opened 3 months ago
0
changed default value of transpose in load_data() function

#45 georgyFenix closed 3 months ago
0
default value of transpose in load_data should be set to False

#44 georgyFenix opened 4 months ago
0
Publication Quality Images

#43 avianalter closed 1 year ago
0
docker image

#42 qisun2 closed 1 year ago
2
KNN Information from sam object

#41 Sayyam-Shah closed 1 year ago
2
compatibility with h5py

#40 galicae closed 2 years ago
3
Harmony with SAM

#39 Sayyam-Shah closed 2 years ago
1
SAM Algorithm - Clusters

#38 Sayyam-Shah closed 2 years ago
4
KeyError: 'connectivities_key' when performing clustering on sam output

#37 chi-raag closed 2 years ago
0
Setting random seed for umap and clustering

#36 suhaasa closed 3 years ago
2
SAM on bbknn merged datasets

#35 kmmika closed 3 years ago
2
Unable to find attributes regress genes

#34 CisnerosFernandez closed 3 years ago
2
problem with sam.show_gene_expression

#33 carlosj-rr closed 3 years ago
3
preprocessing parameters should be set to default like before

#32 atarashansky closed 3 years ago
0
update k-means clustering — currently broken

#31 atarashansky closed 3 years ago
0
Gui multi

#30 atarashansky closed 3 years ago
0
Gui history

#29 atarashansky closed 4 years ago
0
TypeError while running SAM algorithm (cont...)

#28 atarashansky closed 3 years ago
1
issue about the sam.run()

#27 nkm47 closed 4 years ago
9
Be a nice Python citizen

#26 flying-sheep closed 4 years ago
5
TODO: Chunk the nearest neighbor averaging if memory becomes a huge issue

#25 atarashansky closed 3 years ago
1
Try out cUML

#24 atarashansky closed 4 years ago
1
Feature Request: Create a button that lets you compare cluster assignments with heatmap/sankey

#23 atarashansky closed 3 years ago
0
TODO: Add an option to perform PCA on sparse inputs (slower but more memory efficient)

#22 atarashansky closed 4 years ago
1
anndata issue during sam object loading

#20 xuesoso closed 5 years ago
2
TODO: Replace pynndescent with hnswlib

#19 atarashansky closed 4 years ago
1
TODO: add a checkbox to show colorbar or not

#18 atarashansky closed 4 years ago
1
TODO: Check for proper parameters and throw errors.

#17 atarashansky closed 4 years ago
0
Restore option to use matplotlib plotting

#16 andygxzeng closed 5 years ago
2
The weighted gene expression matrix

#15 fenghuijian closed 5 years ago
8
Hi,

#14 fenghuijian closed 5 years ago
12
Feature request: can't copy paste!

#13 dnanes closed 5 years ago
1
Feature request: input of multiple genes

#12 dnanes closed 5 years ago
1
help with removing clusters from clustering analysis

#11 pythonhelp closed 5 years ago
7
Add SAM class specifically designed for large datasets

#10 atarashansky closed 5 years ago
1
Distance matrix error threshold should change w.r.t. the distance metric used

#9 atarashansky closed 5 years ago
1
Include option to set random state

#8 atarashansky closed 5 years ago
0
Reimplement Louvain clustering to avoid reliance on bulky scanpy dependencies.

#7 atarashansky closed 5 years ago
1
More optional deps and Travis works now ;-)

#6 iosonofabio closed 6 years ago
0
Sweep that cruft!

#5 iosonofabio closed 6 years ago
1
Installation stalling at louvain build

#4 BojkArth closed 6 years ago
6
Implement nearest neighbor descent to speed up construction of the NN matrix.

#3 atarashansky closed 5 years ago
1
Travis CI infrastructure

#2 iosonofabio closed 6 years ago
0
singlet integration

#1 iosonofabio closed 6 years ago
21