Ecosyste.ms: Issues

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GitHub / zdebruine/singlet issues and pull requests

#53 - Adds ability to run nmf with new method

Pull Request - State: open - Opened by skyler-ruiter 9 months ago

#52 - Extracting barcodes per component

Issue - State: open - Opened by kmh005 10 months ago - 3 comments

#51 - Clarification on input for NMF -- raw counts or normalized data?

Issue - State: closed - Opened by stephaniehicks 10 months ago - 4 comments

#50 - RunLNMF error: "memory not mapped"

Issue - State: open - Opened by MicTott 10 months ago

#49 - cross_validate_nmf giving NAN tolerance and overfit

Issue - State: open - Opened by cindyfang70 10 months ago - 2 comments

#48 - Compilation Error on Installation

Issue - State: open - Opened by samuel-marsh 10 months ago - 6 comments

#47 - Compatibility with Seurat V5

Issue - State: open - Opened by zdebruine 10 months ago - 1 comment

#46 - Advice for usage of Linked NMF for scATAC

Issue - State: closed - Opened by IsaacDiaz026 11 months ago - 1 comment

#45 - Coerce w and h to matrices when rank=1 (closes #44)

Pull Request - State: closed - Opened by knowah 11 months ago

#44 - run_nmf() fails with rank=1

Issue - State: closed - Opened by knowah 11 months ago

#42 - split.by option in RunNMF

Issue - State: closed - Opened by IsaacDiaz026 12 months ago - 1 comment

#41 - Singlet modifies the original data matrix in the Seurat object

Issue - State: closed - Opened by TaopengWang 12 months ago - 13 comments

#40 - Revert "My PR"

Pull Request - State: closed - Opened by zdebruine about 1 year ago

#39 - Issue with RunNMF on SeuratV5 objects

Issue - State: closed - Opened by jemorlanes about 1 year ago - 12 comments

#38 - My PR

Pull Request - State: closed - Opened by SBaluszek about 1 year ago

#37 - Update run_nmf.R

Pull Request - State: closed - Opened by SBaluszek about 1 year ago

#36 - c_nmf needs number of threads

Issue - State: closed - Opened by SBaluszek about 1 year ago - 2 comments

#35 - RunGSEA getting stuck at 8%

Issue - State: closed - Opened by Prathyusha-konda about 1 year ago - 3 comments

#34 - MetadataPlot needs to drop factor levels with 0 counts

Issue - State: open - Opened by zdebruine about 1 year ago

#33 - Fix AnnotateNMF() bug

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

#32 - cleanup and add coercions

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

#31 - Corner case of RunNMF trying rank 1

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

#30 - AnnotateNMF() does not pass internal checks

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

#29 - remove scuttle dependency

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

#27 - Rlog1p error

Issue - State: closed - Opened by jemorlanes over 1 year ago - 8 comments

#26 - RunGSEA(pbmc3k,verbose = FALSE) gives empty results using example data

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

#25 - class "nmf" is not exported by 'namespace:RcppML'

Issue - State: closed - Opened by shalbahl almost 2 years ago - 8 comments

#24 - fix transpose bug

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

#23 - cleaned up getModelMatrix and getModelFit with new examples for testing

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

#22 - getModelFit throwing error regarding dimnames

Issue - State: closed - Opened by zdebruine almost 2 years ago - 4 comments

#21 - Updated procrustes and Rescaled NMF

Pull Request - State: closed - Opened by Barthur006 about 2 years ago - 1 comment

#20 - "Not a matrix." error when it's definitely a matrix

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

#19 - Fixed a couple of missing/extra variable bugs

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

#18 - Rescaled and Procrutes

Pull Request - State: closed - Opened by Barthur006 about 2 years ago

#17 - Silence protip

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

#16 - added a few more convenience methods for nmf objects

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

#15 - refactored, added list -> nmf coercion for ard_nmf results, etc.

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

#14 - Option to select features for NMF

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

#13 - Fixed k for RunNMF

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

#12 - ard_nmf crashes on segfault (problem occurs in c_nmf_base) for dense data matrix

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

#8 - Importing RcppML in NAMESPACE but not DESCRIPTION

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

#7 - force model fits to annotate against grand means

Pull Request - State: closed - Opened by ttriche over 2 years ago - 1 comment

#6 - RunNMF() error - if (overfit_score == 0) cat(" not overfit\n")

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

#4 - refactored functions for use independently (e.g. on existing nmf objects)

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

#3 - Refactor & document RunNMF/AnnotateNMF/AnnotationPlot; use limma

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

#2 - Overfitting detection and coordinate descent for ARD

Issue - State: closed - Opened by zdebruine over 2 years ago

#1 - Current actions for LNMF functionality

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