Ecosyste.ms: Issues

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GitHub / epigen/unsupervised_analysis issues and pull requests

#51 - enhance Snakemake report using labels

Issue - State: open - Opened by sreichl 6 months ago
Labels: enhancement

#49 - consider PCA parameter of % of variance to keep to speed up for large data

Issue - State: open - Opened by sreichl 6 months ago
Labels: enhancement

#47 - clustification: implement XGBoost

Issue - State: open - Opened by sreichl 6 months ago

#46 - make cluster validation using indices optional

Issue - State: open - Opened by sreichl 9 months ago
Labels: enhancement

#45 - Error plot_dimred_metadata

Issue - State: open - Opened by bednarsky 9 months ago - 1 comment
Labels: bug

#44 - UMAP diagnostics bug - numba intersect1d

Issue - State: open - Opened by bednarsky 9 months ago - 3 comments
Labels: bug

#43 - snakemake找不到srcdir函数

Issue - State: closed - Opened by summersohot 10 months ago - 5 comments
Labels: bug

#41 - diagnostic plot of all aggregated clustering results

Issue - State: open - Opened by sreichl 11 months ago
Labels: enhancement

#40 - fix job selection for cluster indices without clusterings

Issue - State: closed - Opened by sreichl 11 months ago
Labels: bug

#39 - new minor release when adapted to very large data

Issue - State: open - Opened by sreichl 11 months ago
Labels: documentation

#37 - improve data loading speed with Dask or NumPy

Issue - State: open - Opened by sreichl 11 months ago
Labels: enhancement

#36 - improve scatter plot speed

Issue - State: open - Opened by sreichl 11 months ago - 1 comment
Labels: enhancement

#35 - Gene program/marker expression score as metadata

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

#34 - PCA fails for large dataset

Issue - State: closed - Opened by kvetab about 1 year ago - 1 comment
Labels: bug

#32 - utilize metadata of interest config field as list for multiple analyses

Issue - State: closed - Opened by sreichl about 1 year ago
Labels: enhancement

#31 - add Variation of Information (VI) and Split/Join as external indices

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#30 - implement Manifold trustworthiness

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#29 - implement significance analysis for clustering

Issue - State: open - Opened by sreichl about 1 year ago - 1 comment
Labels: enhancement

#28 - clustification: add visualization of performance/convergence over time

Issue - State: open - Opened by sreichl about 1 year ago - 1 comment
Labels: enhancement

#27 - Resampling to evaluate clustering stability

Issue - State: open - Opened by bednarsky about 1 year ago
Labels: enhancement

#26 - investigate PCA OOM error with Lee2020NatGenet data

Issue - State: closed - Opened by sreichl about 1 year ago
Labels: bug

#25 - clustification: test simultaneous merging

Issue - State: closed - Opened by sreichl about 1 year ago - 1 comment
Labels: enhancement

#24 - clustree: investigate and implement automatic sc3 stability scoring

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#23 - change storing and aggregation of clustering results

Issue - State: closed - Opened by sreichl about 1 year ago
Labels: enhancement

#22 - implement consensus cluster calling

Issue - State: open - Opened by sreichl about 1 year ago - 1 comment
Labels: enhancement

#21 - rank all clustering results according to all internal cluster indices using MCDM algorithm

Issue - State: closed - Opened by sreichl about 1 year ago
Labels: enhancement

#19 - test & document

Issue - State: closed - Opened by sreichl about 1 year ago - 4 comments
Labels: documentation

#18 - PCA: additional visualization of top loadings per PC

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#17 - release version 1.0.0

Issue - State: closed - Opened by sreichl about 1 year ago
Labels: enhancement

#16 - implement meta visualization as an aggregation of all methods (PCA, densMAP, UMAP, …)

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#15 - add Dynamic visualization of high-dimensional data

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#14 - implement partition based clustering

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#13 - Consider alternative clustering algorithms

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#12 - clustification: Benchmark clf-based clustering approach

Issue - State: open - Opened by sreichl about 1 year ago - 5 comments
Labels: enhancement

#11 - add quote about clustering to documentation

Issue - State: closed - Opened by sreichl about 1 year ago - 1 comment
Labels: documentation

#10 - implement cluster validation using indices

Issue - State: closed - Opened by sreichl about 1 year ago - 7 comments
Labels: enhancement

#9 - implement parameter-free classifier-approach to clustering

Issue - State: closed - Opened by sreichl about 1 year ago - 6 comments
Labels: enhancement

#8 - Visualize clustering results using clustree

Issue - State: closed - Opened by sreichl about 1 year ago - 3 comments
Labels: enhancement

#7 - Visualize clustering results

Issue - State: closed - Opened by sreichl about 1 year ago
Labels: enhancement

#6 - implement HDBSCAN clustering

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#5 - implement Leiden clustering

Issue - State: closed - Opened by sreichl about 1 year ago - 4 comments
Labels: enhancement

#4 - address slow heatmaps

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#3 - check if sklearn PCA automatically standard scales the data

Issue - State: open - Opened by sreichl about 1 year ago
Labels: enhancement

#2 - document all versions in environment yaml specifications

Issue - State: closed - Opened by sreichl about 1 year ago
Labels: documentation

#1 - feature plot option "all"

Issue - State: open - Opened by sreichl about 1 year ago - 1 comment
Labels: enhancement