JonathanShor/DoubletDetection issues and pull requests

#159 - Remove dependency louvain and leidenalg

Issue - State: open - Opened by dmalzl 2 months ago - 1 comment

#158 - Error for clf.fit

Issue - State: open - Opened by AdotaLover 4 months ago - 4 comments

#157 - `IndexError: list index out of range`

Issue - State: open - Opened by danli349 over 1 year ago

#156 - Input for mixed species experiments

Issue - State: open - Opened by rjg2186 over 1 year ago

#155 - verbose = False

Issue - State: open - Opened by Laolga about 2 years ago - 1 comment

#154 - A bug? Random seed 0 will never be set.

Issue - State: open - Opened by Christina-hshi over 2 years ago

#153 - Dev 4.2

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

#152 - [DO NOT MERGE] Dev 5.0

Pull Request - State: open - Opened by adamgayoso over 2 years ago

#151 - Dev 4.1

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

#150 - remove lock file

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

#149 - Bump pywin32 from 300 to 301

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#148 - Bump babel from 2.9.0 to 2.9.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#147 - Bump urllib3 from 1.26.2 to 1.26.5

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#146 - Bump notebook from 6.1.5 to 6.4.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#145 - update docs

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

#144 - Bump ipython from 7.16.1 to 7.16.3

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#143 - Loading in raw matrix

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

#142 - Memory usage increases when using scanpy clustering

Issue - State: open - Opened by kaylahardwick over 3 years ago - 2 comments

#141 - Memory Error when running.

Issue - State: closed - Opened by Mike0117 almost 4 years ago

#140 - Docs again

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

#139 - Dev 4.0

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

#138 - Docs

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

#137 - Update reference on readme

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

#136 - move to poetry for dist, remove excess code, use pip installable pheno

Pull Request - State: closed - Opened by adamgayoso almost 4 years ago - 1 comment

#135 - Reproducibility issue

Issue - State: closed - Opened by Jayjay601 about 4 years ago

#134 - readme update

Pull Request - State: closed - Opened by adamgayoso over 4 years ago

#133 - List of barcode duplets

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

#132 - got "list index out of range" error

Issue - State: closed - Opened by jchenpku almost 5 years ago - 2 comments

#131 - Dev v2.5.2

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

#130 - Neighbor graph should only be calculated when not using PhenoGraph

Issue - State: closed - Opened by adamgayoso over 5 years ago
Labels: enhancement

#129 - Error for doublet detection

Issue - State: closed - Opened by lh12565 over 5 years ago - 4 comments

#128 - Phenograph params return NA on PBMC8K

Issue - State: closed - Opened by TomKellyGenetics over 5 years ago - 3 comments

#127 - Fix defaults

Pull Request - State: closed - Opened by adamgayoso over 5 years ago

#126 - make readthedocs pass

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

#125 - Dev v2.5

Pull Request - State: closed - Opened by JonathanShor over 5 years ago

#124 - Dev v3.0 -> 2.5

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

#123 - Verbosity

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

#122 - Create coding standards

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

#121 - Documentation and Package Restructure

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

#120 - Allow alternative clustering

Issue - State: closed - Opened by adamgayoso over 5 years ago - 3 comments
Labels: enhancement

#119 - Integrate scanpy for more efficient clustering and general functionality

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

#118 - Sparse raw counts and UMAP

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

#117 - Reduce memory by storing raw_counts as sparse

Issue - State: closed - Opened by adamgayoso over 5 years ago
Labels: enhancement

#116 - Vectorize synths

Pull Request - State: closed - Opened by adamgayoso over 5 years ago

#115 - NaN in doublets score

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

#114 - biorxiv submission?

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

#113 - Cluster of origin for doublets and results interpretation

Issue - State: closed - Opened by danshu about 6 years ago - 2 comments

#112 - Removing default thresholds

Issue - State: closed - Opened by adamgayoso over 6 years ago - 3 comments
Labels: enhancement

#111 - Dev v2.4

Pull Request - State: closed - Opened by adamgayoso over 6 years ago - 1 comment

#110 - Improve plots

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#109 - return PhenoGraph clustering in tsne plot

Issue - State: closed - Opened by adamgayoso over 6 years ago
Labels: enhancement

#108 - scanpy normalization

Issue - State: closed - Opened by adamgayoso over 6 years ago - 8 comments
Labels: enhancement

#107 - Vectorize synthetic doublet creation

Issue - State: closed - Opened by adamgayoso over 6 years ago - 1 comment
Labels: enhancement

#106 - Random seed

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#105 - setting random seed for reproducibility?

Issue - State: closed - Opened by yueqiw over 6 years ago - 3 comments
Labels: enhancement

#104 - tsne plot assumes raw_counts is np.ndarray

Issue - State: closed - Opened by adamgayoso over 6 years ago - 1 comment
Labels: enhancement

#103 - Threshold plot fix

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#102 - Make the log10 P values in threshold plot more intuitive?

Issue - State: closed - Opened by yueqiw over 6 years ago - 19 comments
Labels: enhancement

#101 - Log p-values

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#100 - Clean setup

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#99 - Log p val

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#98 - Any systematic validation/benchmarking of this algorithm?

Issue - State: open - Opened by yueqiw over 6 years ago - 13 comments

#97 - Fix masked labels filling for ambiguous cells

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#96 - Fast(er) Normalize

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#95 - Conforms to #68 when n_iters == 1

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#94 - memory requirement

Issue - State: closed - Opened by lpantano over 6 years ago - 4 comments

#93 - Doublet estimation with Jurkat cell data

Issue - State: closed - Opened by joonlee3 over 6 years ago - 1 comment

#92 - Fast normalize

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#91 - Moved all reqs to requirements.txt and out of setup.py

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#90 - 2.1 review

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#89 - Dev v2.1

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#88 - No downsampling

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#87 - Input formats

Pull Request - State: closed - Opened by adamgayoso over 6 years ago - 2 comments

#86 - Viz v2.1

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#85 - Keeping data-heavy objects after fit

Issue - State: open - Opened by JonathanShor over 6 years ago
Labels: feedback requested

#84 - Set phenograph parameter 'prune'=True by default.

Pull Request - State: closed - Opened by JonathanShor over 6 years ago - 1 comment

#83 - Make prune=True default

Issue - State: closed - Opened by adamgayoso over 6 years ago
Labels: bug

#82 - notebook complies with 2.0 api

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#81 - v2.0 API Stablized

Pull Request - State: closed - Opened by JonathanShor over 6 years ago - 2 comments

#80 - Adds normalizer parameter.

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#79 - Api 2.0

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#78 - Adds attribute top_var_genes.

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#77 - Removed requirement that cluster IDs be bumped up if -1 cluster

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#76 - Api 2.0

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#75 - -1 cluster and updated docstring for BoostClassifier

Pull Request - State: closed - Opened by adamgayoso over 6 years ago - 1 comment

#74 - Run on command line

Issue - State: closed - Opened by adamgayoso over 6 years ago - 2 comments
Labels: enhancement, feedback requested

#73 - Plug-in normalization method

Issue - State: closed - Opened by adamgayoso over 6 years ago
Labels: enhancement

#72 - Mini viz suite

Issue - State: closed - Opened by adamgayoso over 6 years ago
Labels: enhancement

#71 - Input types for count matrix

Issue - State: closed - Opened by adamgayoso over 6 years ago - 2 comments
Labels: enhancement

#70 - Pbmc 8k vignette

Pull Request - State: closed - Opened by adamgayoso over 6 years ago

#69 - Installable Packaging

Pull Request - State: closed - Opened by JonathanShor over 6 years ago
Labels: enhancement

#68 - Improve never clustered warning message

Issue - State: closed - Opened by JonathanShor over 6 years ago - 1 comment
Labels: enhancement

#67 - ENH: reorg into package, make installable

Pull Request - State: closed - Opened by ambrosejcarr over 6 years ago

#66 - ENH: reorg into package, make installable

Pull Request - State: closed - Opened by ambrosejcarr over 6 years ago - 1 comment

#65 - Correct 1 iter & prune warning logic.

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#64 - Verbose options

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

#63 - v1.3 Voting Classification

Pull Request - State: closed - Opened by JonathanShor over 6 years ago - 1 comment

#62 - Voting scheme

Pull Request - State: closed - Opened by JonathanShor over 6 years ago

#61 - Conform to sklearn estimator API

Issue - State: closed - Opened by JonathanShor over 6 years ago - 2 comments

#60 - Exclude unclustered cells from deciding doublets.

Pull Request - State: closed - Opened by JonathanShor over 6 years ago
Labels: bug

GitHub / JonathanShor/DoubletDetection issues and pull requests