plger/scdblfinder issues and pull requests

#113 - Does scDblFinder works in Seurat V5 ?

Issue - State: closed - Opened by lssb 9 days ago

#100 - Error running scDblFinder

Issue - State: closed - Opened by chungsai 8 months ago - 4 comments

#99 - Error running scDblFinder

Issue - State: closed - Opened by dimitrisokolowskei 8 months ago - 7 comments

#98 - How can I add results to back my original file

Issue - State: closed - Opened by karabicicim 9 months ago - 2 comments

#97 - "did not converge" Error on cellbender3

Issue - State: closed - Opened by IrinaVKuznetsova 9 months ago - 8 comments

#96 - Does ‘Size factors should be positive’ error matter?

Issue - State: closed - Opened by YiweiNiu 9 months ago - 4 comments

#95 - error in scATAC

Issue - State: closed - Opened by LidiaML 10 months ago - 1 comment

#94 - Compatibility between Seurat, matrix and scDblFinder versions

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

#93 - Ambient RNA Removal

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

#92 - Unable to install scDblFinder

Issue - State: closed - Opened by CCGOGO12 11 months ago - 2 comments

#91 - Unable to run scDblFinder - "as_cholmod_sparse" does not exist

Issue - State: open - Opened by sunnlife1978 11 months ago - 5 comments

#90 - Doublet filtering in Parse Biosciences data

Issue - State: closed - Opened by kaanokay 12 months ago - 6 comments

#89 - Clarify recommended nFeatures/artificialDoublets for scATACseq doublet removal in vignette

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

#88 - non-interpretable error message when providing non-integer as nfeatures argument

Issue - State: closed - Opened by Fiona713 about 1 year ago - 1 comment

#87 - Error running scDblFinder

Issue - State: closed - Opened by malonzm1 about 1 year ago - 3 comments

#86 - Running scDblFinder before or after normalization?

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

#85 - Fix vaeda link

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

#84 - Unreasonably high doublets rate

Issue - State: closed - Opened by t-nol about 1 year ago - 4 comments

#83 - Error in as(counts(sce), "CsparseMatrix")

Issue - State: closed - Opened by akhst7 about 1 year ago - 1 comment

#82 - scDblFinder error when using aggregateFeatures and knownDoublets

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

#81 - Running into Grid Error when Running scDblFinder

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

#80 - Request for clarification of dbr and dbr.sd in scDblFinder 1.15.1

Issue - State: closed - Opened by aghr over 1 year ago - 4 comments

#79 - Runing scDblFinder before and after removing low QC cells gives different results

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

#78 - Error in if (length(expected) > 1 && x > min(expected) && x < max(expected)) return(0): missing value where TRUE/FALSE needed

Issue - State: closed - Opened by twoneu over 1 year ago - 18 comments

#77 - Error when running library(scDblFinder) on jupyter through %%R

Issue - State: closed - Opened by ngvananh2508 over 1 year ago - 2 comments

#76 - Filter ATAC before running scDblFinder

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

#75 - did not converge

Issue - State: closed - Opened by z5ouyang over 1 year ago - 5 comments

#74 - I'm having an issues with sctransform not sure

Issue - State: closed - Opened by zvan14 over 1 year ago - 1 comment

#73 - error in serialize(data)

Issue - State: closed - Opened by wbvguo over 1 year ago - 6 comments

#72 - Installing scDblFinder with conda not working

Issue - State: closed - Opened by dimitrisokolowskei over 1 year ago - 6 comments

#71 - Return threshold in output?

Issue - State: closed - Opened by maryellenlynall over 1 year ago - 4 comments

#70 - scDblFinder - known doublets

Issue - State: closed - Opened by maryellenlynall over 1 year ago - 6 comments

#69 - Unreasonably high doublets rate

Issue - State: closed - Opened by zqun1 over 1 year ago - 6 comments

#68 - Merging multiple samples with scATAC prior to scDblFinder

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

#67 - doublets mostly differ between scDblFinder and doubletFinder

Issue - State: closed - Opened by gianfilippo almost 2 years ago - 18 comments

#66 - scDbliFinder.sample is different from the sample column specified in `scDblFinder` function `samples` column ?

Issue - State: closed - Opened by Yunuuuu almost 2 years ago - 17 comments

#65 - Import default hyperparams from Xi and Vasilopoulos

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

#64 - Optimal Hyperparameter

Pull Request - State: closed - Opened by xnnba1984 almost 2 years ago

#63 - Deprecated "dgcMatrix"

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

#62 - Doublet numbers still not reproduced even though I used BPPARAM and bpstart

Issue - State: closed - Opened by Moonju411 about 2 years ago - 2 comments

#61 - How to find all features used in training

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

#60 - Error in installing scDblFinder: object ‘colBlockApply’ is not exported by 'namespace:beachmat'

Issue - State: closed - Opened by amber4mint about 2 years ago - 5 comments

#59 - Running scDblFinder deterministic and serial with the 'samples' parameter

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

#58 - V minor coding bug with multiSampleMode = 'split' and returnType = 'table'

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

#57 - Possible Bug: cxds2 call does not include artificial doublets in whichDbls

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

#56 - why error ?

Issue - State: closed - Opened by kdyoung100 over 2 years ago - 4 comments

#55 - size factors should be positive in computeDoubletDensity

Issue - State: closed - Opened by Close-your-eyes over 2 years ago - 1 comment

#54 - xcgboost install

Issue - State: closed - Opened by bjstewart1 over 2 years ago - 2 comments

#53 - scDblFinder not deterministic when using batch+BPPARAM

Issue - State: closed - Opened by ATpoint almost 3 years ago - 9 comments

#52 - Exploring Overrepresented Doublets

Issue - State: closed - Opened by cohenp05 almost 3 years ago - 3 comments

#51 - Issue running scDblFinder on scATAC-seq data

Issue - State: closed - Opened by debbie28 almost 3 years ago - 3 comments

#50 - BiocParallel error - could not find symbol 'useNames' in environment of the generic function

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

#49 - Forgot to import sweep from DelayedArray

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

#48 - Feats4bm

Pull Request - State: closed - Opened by plger over 3 years ago

#47 - Feats4bm

Pull Request - State: closed - Opened by plger over 3 years ago

#46 - Dimension reduction option

Issue - State: closed - Opened by bjstewart1 over 3 years ago - 2 comments

#45 - Issue with knownDoublets

Issue - State: closed - Opened by bjstewart1 over 3 years ago - 3 comments

#44 - No mbkmeans requirement + fixed doc params

Pull Request - State: closed - Opened by plger over 3 years ago

#43 - Using both scATAC and scGEX combined from 10x Multiome for doublet calling

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

#42 - Update scDblFinder.R

Pull Request - State: closed - Opened by federicomarini over 3 years ago

#41 - Error in sample.int(length(x), size, replace, prob)

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

#40 - Pre-filter the count matrix before scDblFinder?

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

#39 - Merge data or individual data

Issue - State: closed - Opened by ysu2015 over 3 years ago - 2 comments

#38 - Batch mode with BPPARAM=MulticoreParam() not working

Issue - State: closed - Opened by JTpath over 3 years ago - 15 comments

#37 - Error in ecdf(d$cxds_score[w]) : 'x' must have 1 or more non-missing values

Issue - State: closed - Opened by lindsaynhayes over 3 years ago - 9 comments

#36 - fixed some warnings in devel check

Pull Request - State: closed - Opened by plger over 3 years ago

#35 - Installing fails as requires R 4.1.0

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

#34 - added feature aggregation for scATAC

Pull Request - State: closed - Opened by plger over 3 years ago

#33 - Multi sample mode

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

#32 - Size factors should be positive

Issue - State: closed - Opened by Yale73 almost 4 years ago - 6 comments

#31 - Error with empty factor levels

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

#30 - "griffiths" threshold measure should not be per-cluster

Issue - State: closed - Opened by jonathangriffiths almost 4 years ago - 5 comments

#29 - Refer to the right internal function in tests.

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

#28 - Note to self: figure out why computeDoubletDensity is unhappy on R-devel

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

#27 - rowMeans Error

Issue - State: closed - Opened by drneavin about 4 years ago - 5 comments

#26 - Miscellaneous clustering observations

Issue - State: closed - Opened by LTLA about 4 years ago - 8 comments

#25 - probs outside [0,1] when training model

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

#24 - port changes from devel

Pull Request - State: closed - Opened by plger about 4 years ago

#23 - rbind error when running multiple samples

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

#22 - port master to devel

Pull Request - State: closed - Opened by plger about 4 years ago

#21 - scDblFinder.class no longer added to SCE output

Issue - State: closed - Opened by j-andrews7 about 4 years ago - 2 comments

#20 - Fixed computeDoubletDensity.

Pull Request - State: closed - Opened by LTLA about 4 years ago

#19 - Assorted fixes to vignettes

Pull Request - State: closed - Opened by LTLA about 4 years ago

#18 - Actually added the vignette for recoverDoublets theory.

Pull Request - State: closed - Opened by LTLA about 4 years ago

#17 - Devel

Pull Request - State: closed - Opened by plger about 4 years ago