swolock/scrublet issues and pull requests

#63 - FIX for numpy2.0.2

Issue - State: closed - Opened by andynkili 2 months ago

#62 - Does scrublet change the barcode names?

Issue - State: open - Opened by st4302 3 months ago

#61 - scrub.scrub_doublets() hangs

Issue - State: open - Opened by obrien-james 8 months ago - 1 comment

#60 - does scrublet work with 10X fixed rna profiling?

Issue - State: open - Opened by tea-egg-sheldon 10 months ago

#59 - Doubets do not occupy distinct states

Issue - State: open - Opened by AAA-3 about 1 year ago

#58 - Question normalize_variance

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

#57 - Non-sparse intermediate result causes huge uptick in memory use

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

#56 - Scrublet runs into an endless loop

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

#55 - Export scrublet plots to .png or .pdf files

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

#54 - Multiplets after scrublet?

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

#53 - Doublet for mixed species

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

#52 - pip install error in windows anaconda prompt

Issue - State: open - Opened by archana433 almost 2 years ago - 2 comments

#51 - Will there be a version compatible with python 3.9?

Issue - State: open - Opened by havu73 almost 2 years ago

#50 - Illegal instruction core dumped error

Issue - State: open - Opened by PDhingra2016 almost 2 years ago - 2 comments

#49 - input data with pearson residuals workflow

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

#48 - output file with cell barcodes?

Issue - State: open - Opened by azwainCC over 2 years ago

#47 - Number genes value is different

Issue - State: open - Opened by IlianCx over 2 years ago

#46 - Kernel died when running scrublet

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

#45 - Potential mistake: percentile vs quantile

Issue - State: open - Opened by iaaka over 2 years ago

#44 - The result shows that there is only one double cell, but there are many on umap

Issue - State: open - Opened by ouyangcuihuaa over 2 years ago

#43 - pip install error

Issue - State: open - Opened by ulloaa almost 3 years ago - 2 comments

#42 - How to delete doublets from Seurat object

Issue - State: open - Opened by GreyRockIQ almost 3 years ago - 1 comment

#41 - Do I use scrublet after doing the standard preprocessing from Seurat?

Issue - State: open - Opened by st4302 almost 3 years ago - 1 comment

#40 - Error: ValueError: Expected 1D or 2D array, got 0D array instead

Issue - State: open - Opened by TingtingSsl2 almost 3 years ago - 1 comment

#39 - Threshold setting on non bimodal simulated doublet score distribution

Issue - State: open - Opened by liliay almost 3 years ago

#38 - Rolling back uninstall of llvmlite

Issue - State: open - Opened by brianpenghe almost 3 years ago - 2 comments

#37 - Running error with scrub.plot_embedding

Issue - State: closed - Opened by lwlive almost 3 years ago - 2 comments

#36 - ImportError when using scrublet with reticulate (R studio)

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

#35 - Scrublet in development atlas

Issue - State: open - Opened by DiracZhu1998 about 3 years ago

#34 - scrub_doublets still completes without annoy, nearest neighbor search

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

#33 - Installation issue

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

#32 - import error: file_hash from pooch.util

Issue - State: open - Opened by JustinYeon over 3 years ago

#31 - Scrublet disables my figures

Issue - State: open - Opened by ChaseTaylor939 over 3 years ago - 2 comments

#30 - How to set the 'expected_doublet_rate' in Scrublet?

Issue - State: open - Opened by victorwang123 over 3 years ago - 1 comment

#29 - How to use the results of scrublet?

Issue - State: open - Opened by victorwang123 over 3 years ago

#28 - scrublet doesn't work properly

Issue - State: open - Opened by huwenrime almost 4 years ago - 1 comment

#27 - Can I use the xxx.rds as the input file? Thank you!

Issue - State: open - Opened by loubean4073 almost 4 years ago

#26 - AttributeError while loading gene list

Issue - State: open - Opened by ishwarvh almost 4 years ago - 9 comments

#25 - "import scrublet as scr" error

Issue - State: open - Opened by danielcgingerich almost 4 years ago - 1 comment

#24 - Can't run scrublet successfully with command 'scrub.plot_embedding'

Issue - State: closed - Opened by wangjunyu-cumt over 4 years ago

#23 - Scrublet takes very long time to run

Issue - State: open - Opened by liron27 over 4 years ago - 1 comment

#22 - Segmentation fault when scrub.set_embedding

Issue - State: open - Opened by yingyonghui over 4 years ago

#21 - Is there a R version of scrublet on the way?

Issue - State: open - Opened by yingyonghui over 4 years ago - 1 comment

#20 - [bug] Plot doublet predictions

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

#19 - Threshold to call doublets

Issue - State: open - Opened by Jayjay601 over 4 years ago - 1 comment

#18 - Memory Error when running scrublet

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

#17 - Providing source populations of doublets for annotated datasets

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

#16 - Unimodal distributions, log transformation, and homogeneous data sets

Issue - State: open - Opened by aaron-allen over 4 years ago

#15 - potential cross validation of predicted doublets

Issue - State: open - Opened by MichaelPeibo almost 5 years ago - 2 comments

#14 - Expected doublet rate question

Issue - State: open - Opened by s849 almost 5 years ago - 1 comment

#13 - Finding the right threshold for `call_doublets'

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

#12 - Errorn when calculating doublet scores

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

#11 - Which python version did this scrublet used?

Issue - State: closed - Opened by Lucyyang1991 almost 5 years ago - 1 comment

#10 - scATAC data

Issue - State: open - Opened by TheSallyGardens about 5 years ago - 2 comments

#9 - Use PCA svd_solver = 'arpack' method for reproducibility

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

#8 - Minor upkeep

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

#7 - Not reproducible

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

#6 - SVD instead of PCA

Issue - State: open - Opened by DanSchnell almost 6 years ago - 2 comments

#5 - Export scrublet results

Issue - State: open - Opened by hamishking almost 6 years ago - 14 comments

#4 - issue with `_validate_lengths`: needed to downgrade to `numpy 1.15`

Issue - State: open - Opened by aopisco almost 6 years ago - 1 comment

#3 - scrublet histogram is not bimodal

Issue - State: open - Opened by grst about 6 years ago - 10 comments

#2 - Parameter K for K-nearest neighbor algorithm

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

#1 - first release

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

GitHub / swolock/scrublet issues and pull requests