Ecosyste.ms: Issues

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GitHub / Teichlab/bbknn issues and pull requests

#62 - error in import of DistanceMetric

Issue - State: open - Opened by mahogny about 1 month ago - 1 comment

#61 - BBKNN for ATAC data

Issue - State: open - Opened by wlason 4 months ago - 1 comment

#60 - kernals died when using bbknn

Issue - State: closed - Opened by FessenSimon 6 months ago - 2 comments

#59 - Update on bioconda

Issue - State: closed - Opened by benjamin-james 12 months ago - 2 comments

#58 - np.matrix and ridge_regression

Issue - State: closed - Opened by maryellenlynall about 1 year ago - 5 comments

#57 - Enable Faiss with GPU support.

Pull Request - State: closed - Opened by canergen over 1 year ago - 3 comments

#55 - Fix `ImportError` for `scikit_learn` >=1.0.0

Pull Request - State: closed - Opened by matchy233 over 1 year ago

#54 - `ImportError` for `scikit_learn` >= 1.0.0

Issue - State: closed - Opened by matchy233 over 1 year ago - 9 comments

#53 - error during ridge_regression

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

#52 - BBKNN incompatible with 'x86_64', need 'arm64e'

Issue - State: open - Opened by Shaun-Regenbaum over 1 year ago - 3 comments

#51 - Query cells together

Pull Request - State: closed - Opened by ChuanXu1 about 2 years ago - 1 comment

#50 - Issues importing bbknn after successful install

Issue - State: closed - Opened by ngolan1 about 3 years ago

#49 - Feature/parallel graphs

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

#48 - ValueError: No hyperplanes of adequate size were found! When not using annoy

Issue - State: open - Opened by mtvector about 3 years ago - 5 comments

#47 - Performace varied on different operating systems

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

#46 - Removing multiple covariates during integration

Issue - State: closed - Opened by connorhknight about 3 years ago - 1 comment

#45 - Export BBKNN results to R software

Issue - State: closed - Opened by edroaldo over 3 years ago - 1 comment

#44 - incompatible with annoy==1.17.0 ?

Issue - State: open - Opened by zktuong over 3 years ago - 1 comment

#43 - Does bbknn really work?

Issue - State: closed - Opened by HelloWorldLTY over 3 years ago - 4 comments

#42 - problem : name 'logg' is not defined

Issue - State: closed - Opened by Ahmed-fub over 3 years ago - 3 comments

#41 - `n_trees` is now `annoy_n_trees`

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

#40 - considering using `pynndescent` for appox nn search?

Issue - State: closed - Opened by giovp over 3 years ago - 4 comments
Labels: enhancement

#39 - neighbors_within_batch argument usage in R?

Issue - State: closed - Opened by rwelling520 over 3 years ago - 4 comments

#38 - KeyError: 'connectivities' while running running UMAP function

Issue - State: closed - Opened by aditisk over 3 years ago - 1 comment

#37 - add initial distance matrix work

Pull Request - State: open - Opened by olgabot almost 4 years ago

#36 - Add cosine distance as valid metric

Pull Request - State: open - Opened by olgabot almost 4 years ago - 4 comments

#35 - Black formatting

Pull Request - State: open - Opened by olgabot almost 4 years ago

#34 - An error when running bbknn$bbknn(adata,batch_key=0)

Issue - State: open - Opened by Zhaohui-Ruan almost 4 years ago

#33 - Details for pbmc dataset used #30

Issue - State: closed - Opened by mohit1997 almost 4 years ago - 1 comment

#32 - IndexError: index 2 is out of bounds for axis 0 with size 2

Issue - State: closed - Opened by brianpenghe almost 4 years ago - 2 comments
Labels: bug

#31 - TypeError: info() got an unexpected keyword argument 'r

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

#30 - Details for pbmc dataset used

Issue - State: closed - Opened by mohit1997 about 4 years ago - 2 comments

#29 - bbknn spark error when runing with data integrated from scRNA data

Issue - State: closed - Opened by honghh2018 over 4 years ago - 1 comment
Labels: wontfix

#28 - umap error after package updates

Issue - State: closed - Opened by PaulingLiu over 4 years ago - 1 comment

#27 - Please also require packaging in setup.py

Issue - State: closed - Opened by jenzopr over 4 years ago - 2 comments
Labels: bug

#26 - scanpy update incompatibility

Issue - State: closed - Opened by bjstewart1 over 4 years ago - 1 comment
Labels: duplicate

#24 - X_umap_3D

Issue - State: closed - Opened by JBreunig over 4 years ago - 1 comment
Labels: question

#23 - "sklearn" as a dependency

Issue - State: closed - Opened by deto over 4 years ago - 1 comment
Labels: bug

#22 - make connectivity compatible with umap learn 0.4

Pull Request - State: closed - Opened by iandriver almost 5 years ago - 1 comment

#21 - ModuleNotFoundError

Issue - State: closed - Opened by mvfki almost 5 years ago - 1 comment
Labels: invalid

#20 - Allow usage of other embeddings

Pull Request - State: closed - Opened by dawe almost 5 years ago - 2 comments

#19 - Understanding `neighbors_within_batch` parameter?

Issue - State: closed - Opened by chris-rands almost 5 years ago - 1 comment
Labels: question

#18 - Correcting for more than 1 covariate using BBKNN

Issue - State: closed - Opened by dnehar about 5 years ago - 1 comment
Labels: question

#17 - Collaboration

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

#16 - scanpy logging: warn -> warning

Pull Request - State: closed - Opened by fbnrst over 5 years ago - 1 comment

#15 - Logging error

Issue - State: closed - Opened by ivirshup over 5 years ago - 6 comments

#14 - Throwing exceptions with logg.info() arguments.

Pull Request - State: closed - Opened by milescsmith over 5 years ago - 2 comments

#13 - Update access of obsm keys

Pull Request - State: closed - Opened by ivirshup over 5 years ago - 3 comments

#12 - save_knn

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

#11 - Add LICENSE file to MANIFEST.in

Pull Request - State: closed - Opened by jenzopr over 5 years ago - 6 comments

#10 - Bandwidth parameter no longer supported by scanpy or UMAP

Issue - State: closed - Opened by ivirshup over 5 years ago - 7 comments
Labels: bug

#9 - bbknn.bbknn_pca_matrix() output is different from that of bbknn.bbknn()

Issue - State: closed - Opened by NikTuzov almost 6 years ago - 3 comments

#8 - Is it possible to identify marker genes?

Issue - State: closed - Opened by NikTuzov almost 6 years ago - 5 comments
Labels: question

#7 - error reproducing notebook

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

#6 - Any plan on making R package for bbknn?

Issue - State: closed - Opened by MJ-Yang about 6 years ago - 1 comment
Labels: enhancement

#5 - bbknn publication

Issue - State: closed - Opened by wangjiawen2013 about 6 years ago - 1 comment
Labels: question

#4 - bbknn for a subset of the anndata

Issue - State: closed - Opened by aopisco about 6 years ago - 1 comment
Labels: question

#3 - scanorama bbknn

Issue - State: closed - Opened by wangjiawen2013 about 6 years ago - 3 comments
Labels: question

#2 - edge weights

Issue - State: closed - Opened by wangjiawen2013 about 6 years ago - 3 comments
Labels: question

#1 - Standalone function

Issue - State: closed - Opened by ilyakorsunsky over 6 years ago - 4 comments
Labels: enhancement