Ecosyste.ms: Issues

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GitHub / emdann/milopy issues and pull requests

#49 - Feature request: Neighborhood groups in milopy

Issue - State: open - Opened by MaximilianNuber 2 months ago

#49 - Feature request: Neighborhood groups in milopy

Issue - State: open - Opened by MaximilianNuber 2 months ago

#48 - Using different latent space and knn for milo analysis

Issue - State: open - Opened by revolvefire 6 months ago - 2 comments

#48 - Using different latent space and knn for milo analysis

Issue - State: open - Opened by revolvefire 6 months ago - 2 comments

#46 - error with milo.count_nhoods(adata, sample_col="sample")

Issue - State: closed - Opened by yebo085 11 months ago - 2 comments

#46 - error with milo.count_nhoods(adata, sample_col="sample")

Issue - State: closed - Opened by yebo085 11 months ago - 2 comments

#45 - Fix 'X' was used for kNN

Pull Request - State: closed - Opened by canergen over 1 year ago - 1 comment

#45 - Fix 'X' was used for kNN

Pull Request - State: closed - Opened by canergen over 1 year ago - 1 comment

#44 - milo.make_nhoods(combined_emb) fails if 'X' was used for nearest neighbors

Issue - State: closed - Opened by canergen over 1 year ago - 1 comment

#44 - milo.make_nhoods(combined_emb) fails if 'X' was used for nearest neighbors

Issue - State: closed - Opened by canergen over 1 year ago - 1 comment

#43 - make_nhoods Error: Mean of empty slice.

Issue - State: open - Opened by jflusche over 1 year ago - 2 comments

#43 - make_nhoods Error: Mean of empty slice.

Issue - State: open - Opened by jflusche over 1 year ago - 2 comments

#42 - Fix annotate_nhoods

Pull Request - State: closed - Opened by emdann over 1 year ago

#42 - Fix annotate_nhoods

Pull Request - State: closed - Opened by emdann over 1 year ago

#41 - annotate_nhood error

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

#41 - annotate_nhood error

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

#40 - DA_nhoods() .iteritems deprecated

Issue - State: closed - Opened by james-cranley over 1 year ago - 3 comments

#40 - DA_nhoods() .iteritems deprecated

Issue - State: closed - Opened by james-cranley over 1 year ago - 3 comments

#39 - convert annotation_labels to list at time of storing

Pull Request - State: closed - Opened by ktpolanski over 1 year ago - 1 comment

#39 - convert annotation_labels to list at time of storing

Pull Request - State: closed - Opened by ktpolanski over 1 year ago - 1 comment

#38 - plotNhoodExpressionDA in milopy?

Issue - State: open - Opened by ilibarra almost 2 years ago

#38 - plotNhoodExpressionDA in milopy?

Issue - State: open - Opened by ilibarra almost 2 years ago

#37 - Fixed lib_size filtering in DA_nhoods

Pull Request - State: closed - Opened by emdann almost 2 years ago

#37 - Fixed lib_size filtering in DA_nhoods

Pull Request - State: closed - Opened by emdann almost 2 years ago

#36 - Bug: errors if no cells covered for a certain sample

Issue - State: closed - Opened by emdann almost 2 years ago

#36 - Bug: errors if no cells covered for a certain sample

Issue - State: closed - Opened by emdann almost 2 years ago

#35 - Interpret the clustering result

Issue - State: closed - Opened by ZhenjiangFan almost 2 years ago - 2 comments

#35 - Interpret the clustering result

Issue - State: closed - Opened by ZhenjiangFan almost 2 years ago - 2 comments

#34 - Error in make_nhoods if the reduced dims are in pandas.DataFrame

Issue - State: open - Opened by emdann almost 2 years ago - 1 comment

#34 - Error in make_nhoods if the reduced dims are in pandas.DataFrame

Issue - State: open - Opened by emdann almost 2 years ago - 1 comment

#33 - AttributeError: recarray has no attribute columns

Issue - State: open - Opened by PGmajev almost 2 years ago

#33 - AttributeError: recarray has no attribute columns

Issue - State: open - Opened by PGmajev almost 2 years ago

#32 - Get all cells of a neighborhood given the index_cell

Issue - State: closed - Opened by vronii-k about 2 years ago - 2 comments

#32 - Get all cells of a neighborhood given the index_cell

Issue - State: closed - Opened by vronii-k about 2 years ago - 2 comments

#31 - Assigning neighbors_key in milopy.core.make_nhoods

Issue - State: closed - Opened by ghost about 2 years ago - 1 comment

#31 - Assigning neighbors_key in milopy.core.make_nhoods

Issue - State: closed - Opened by ghost about 2 years ago - 1 comment

#30 - Misc bug fixes

Pull Request - State: closed - Opened by emdann about 2 years ago

#30 - Misc bug fixes

Pull Request - State: closed - Opened by emdann about 2 years ago

#29 - Where can I find the information about to which neighborhood a cell belongs

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

#29 - Where can I find the information about to which neighborhood a cell belongs

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

#27 - Fix breaking change to SpatialFDR with pandas 1.5

Pull Request - State: closed - Opened by emdann over 2 years ago

#27 - Fix breaking change to SpatialFDR with pandas 1.5

Pull Request - State: closed - Opened by emdann over 2 years ago

#26 - Refactoring with MuData

Pull Request - State: open - Opened by emdann over 2 years ago - 5 comments

#26 - Refactoring with MuData

Pull Request - State: open - Opened by emdann over 2 years ago - 5 comments

#25 - trying a new test

Pull Request - State: closed - Opened by emdann over 2 years ago

#25 - trying a new test

Pull Request - State: closed - Opened by emdann over 2 years ago

#24 - bump to v0.1.0

Pull Request - State: closed - Opened by emdann over 2 years ago

#24 - bump to v0.1.0

Pull Request - State: closed - Opened by emdann over 2 years ago

#23 - Merge branch 'master' of github.com:emdann/milopy into devel

Pull Request - State: closed - Opened by emdann over 2 years ago

#23 - Merge branch 'master' of github.com:emdann/milopy into devel

Pull Request - State: closed - Opened by emdann over 2 years ago

#22 - autoapi

Pull Request - State: closed - Opened by emdann over 2 years ago

#22 - autoapi

Pull Request - State: closed - Opened by emdann over 2 years ago

#21 - building API

Pull Request - State: closed - Opened by emdann over 2 years ago

#21 - building API

Pull Request - State: closed - Opened by emdann over 2 years ago

#20 - fixing bug in vscode-notebook kernelspec

Pull Request - State: closed - Opened by emdann over 2 years ago

#19 - updated docs requirements

Pull Request - State: closed - Opened by emdann over 2 years ago

#18 - updated conf for rtd

Pull Request - State: closed - Opened by emdann over 2 years ago

#17 - added sphinx docs

Pull Request - State: closed - Opened by emdann over 2 years ago

#16 - Misc plotting improvements and small fixes

Pull Request - State: closed - Opened by emdann over 2 years ago

#15 - fixed intercept issue when specifying contrasts

Pull Request - State: closed - Opened by emdann over 2 years ago

#14 - fix error when specifying KNN graph key

Pull Request - State: closed - Opened by emdann over 2 years ago

#12 - Adding I/O utils and some small fixes

Pull Request - State: closed - Opened by emdann over 2 years ago

#11 - ValueError: Length mismatch

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

#10 - Small fixes for subsetting and future proofing

Pull Request - State: closed - Opened by emdann over 2 years ago

#9 - added function to aggregate continuous variables on nhoods

Pull Request - State: closed - Opened by emdann over 2 years ago

#8 - Fixing conversion breaking DA_nhoods with rpy2>=3.5

Pull Request - State: closed - Opened by emdann over 2 years ago

#7 - plotNhoodGraphDA in python version

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

#6 - Retrieving adata.obs_names belonging to each adata.uns["nhood_adata"].obs_names

Issue - State: closed - Opened by castaway1990 almost 3 years ago - 3 comments

#5 - Unable to save adata.uns["nhood_adata"]

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

#4 - Can't use model.contrasts with categorical variables

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

#3 - added option to set contrasts in DA testing

Pull Request - State: closed - Opened by emdann about 3 years ago

#2 - Native python implementation for NB-GLM instead of `edgeR`

Issue - State: open - Opened by emdann over 3 years ago - 9 comments

#1 - Fix DA_nhoods warning from rpy2

Issue - State: closed - Opened by emdann over 3 years ago