atarashansky/self-assembling-manifold issues and pull requests

#47 - haromy using scanpy external.sam

Issue - State: closed - Opened by Marwansha 3 months ago

#46 - Division by zero warning during sum_norm

Issue - State: open - Opened by georgyFenix 4 months ago

#45 - changed default value of transpose in load_data() function

Pull Request - State: closed - Opened by georgyFenix 4 months ago

#44 - default value of transpose in load_data should be set to False

Issue - State: open - Opened by georgyFenix 4 months ago

#43 - Publication Quality Images

Issue - State: closed - Opened by avianalter over 1 year ago

#42 - docker image

Issue - State: closed - Opened by qisun2 over 1 year ago - 2 comments

#41 - KNN Information from sam object

Issue - State: closed - Opened by Sayyam-Shah over 1 year ago - 2 comments

#40 - compatibility with h5py

Issue - State: closed - Opened by galicae about 2 years ago - 3 comments

#39 - Harmony with SAM

Issue - State: closed - Opened by Sayyam-Shah over 2 years ago - 1 comment

#38 - SAM Algorithm - Clusters

Issue - State: closed - Opened by Sayyam-Shah over 2 years ago - 4 comments

#37 - KeyError: 'connectivities_key' when performing clustering on sam output

Issue - State: closed - Opened by chi-raag almost 3 years ago

#36 - Setting random seed for umap and clustering

Issue - State: closed - Opened by suhaasa about 3 years ago - 2 comments

#35 - SAM on bbknn merged datasets

Issue - State: closed - Opened by kmmika about 3 years ago - 2 comments

#34 - Unable to find attributes regress genes

Issue - State: closed - Opened by CisnerosFernandez over 3 years ago - 2 comments

#33 - problem with sam.show_gene_expression

Issue - State: closed - Opened by carlosj-rr over 3 years ago - 3 comments

#32 - preprocessing parameters should be set to default like before

Issue - State: closed - Opened by atarashansky almost 4 years ago

#31 - update k-means clustering — currently broken

Issue - State: closed - Opened by atarashansky almost 4 years ago

#30 - Gui multi

Pull Request - State: closed - Opened by atarashansky almost 4 years ago

#29 - Gui history

Pull Request - State: closed - Opened by atarashansky about 4 years ago

#28 - TypeError while running SAM algorithm (cont...)

Issue - State: closed - Opened by atarashansky about 4 years ago - 1 comment

#27 - issue about the sam.run()

Issue - State: closed - Opened by nkm47 over 4 years ago - 9 comments

#26 - Be a nice Python citizen

Issue - State: closed - Opened by flying-sheep almost 5 years ago - 5 comments

#25 - TODO: Chunk the nearest neighbor averaging if memory becomes a huge issue

Issue - State: closed - Opened by atarashansky almost 5 years ago - 1 comment

#24 - Try out cUML

Issue - State: closed - Opened by atarashansky almost 5 years ago - 1 comment

#23 - Feature Request: Create a button that lets you compare cluster assignments with heatmap/sankey

Issue - State: closed - Opened by atarashansky almost 5 years ago

#22 - TODO: Add an option to perform PCA on sparse inputs (slower but more memory efficient)

Issue - State: closed - Opened by atarashansky almost 5 years ago - 1 comment

#20 - anndata issue during sam object loading

Issue - State: closed - Opened by xuesoso about 5 years ago - 2 comments

#19 - TODO: Replace pynndescent with hnswlib

Issue - State: closed - Opened by atarashansky about 5 years ago - 1 comment

#18 - TODO: add a checkbox to show colorbar or not

Issue - State: closed - Opened by atarashansky about 5 years ago - 1 comment

#17 - TODO: Check for proper parameters and throw errors.

Issue - State: closed - Opened by atarashansky about 5 years ago

#16 - Restore option to use matplotlib plotting

Issue - State: closed - Opened by andygxzeng over 5 years ago - 2 comments

#15 - The weighted gene expression matrix

Issue - State: closed - Opened by fenghuijian over 5 years ago - 8 comments

#14 - Hi,

Issue - State: closed - Opened by fenghuijian over 5 years ago - 12 comments

#13 - Feature request: can't copy paste!

Issue - State: closed - Opened by dnanes over 5 years ago - 1 comment

#12 - Feature request: input of multiple genes

Issue - State: closed - Opened by dnanes over 5 years ago - 1 comment

#11 - help with removing clusters from clustering analysis

Issue - State: closed - Opened by pythonhelp almost 6 years ago - 7 comments

#10 - Add SAM class specifically designed for large datasets

Issue - State: closed - Opened by atarashansky about 6 years ago - 1 comment

#9 - Distance matrix error threshold should change w.r.t. the distance metric used

Issue - State: closed - Opened by atarashansky about 6 years ago - 1 comment

#8 - Include option to set random state

Issue - State: closed - Opened by atarashansky about 6 years ago

#7 - Reimplement Louvain clustering to avoid reliance on bulky scanpy dependencies.

Issue - State: closed - Opened by atarashansky about 6 years ago - 1 comment

#6 - More optional deps and Travis works now ;-)

Pull Request - State: closed - Opened by iosonofabio about 6 years ago

#5 - Sweep that cruft!

Pull Request - State: closed - Opened by iosonofabio about 6 years ago - 1 comment

#4 - Installation stalling at louvain build

Issue - State: closed - Opened by BojkArth about 6 years ago - 6 comments

GitHub / atarashansky/self-assembling-manifold issues and pull requests