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zijianni
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SpotClean
R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
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Request: git-tag your versions
#31
aowenson-imm
opened
1 month ago
0
Applied for Stereoseq or not
#30
oyxf
opened
1 month ago
0
Spotclean() stalls on testdata
#29
KarolineHoller
opened
5 months ago
2
Error in keepHighGene(raw_ts_data, verbose = verbose) : no slot of name "meta.data" for this object of class "Assay"
#28
Urology-weiyu
closed
8 months ago
5
Ensembl IDs to Gene Names
#27
shahrozeabbas
closed
8 months ago
0
Error: non-finite value supplied by optim
#26
shahrozeabbas
opened
9 months ago
7
Package updates for Seurat v5
#25
zijianni
closed
10 months ago
0
Update for new Bioconductor release
#24
zijianni
closed
10 months ago
0
SpotClean performance on 11x11mm slides and questions regarding to output
#23
Streisenberg
closed
9 months ago
1
Prepare for upcoming Seurat v5 release
#22
Gesmira
closed
9 months ago
1
Error in convertToSeurat function, "Error in FUN(left, right) : non-numeric argument to binary operator"
#21
maki8080
closed
10 months ago
2
The tissue photographs were presented in the wrong horizontal and vertical ratio
#20
BourbonZhang
closed
1 year ago
2
Error in createSlide(), 'barcodes in count matrix do not match barcodes in slide info'
#19
BartBryant
closed
1 year ago
9
How to run with large datasets in limited memory?
#18
ZeroLi-Bio
closed
1 year ago
2
The "max difference of decontaminated expressions"
#17
Peevin
closed
1 year ago
4
could spotclean work under situation that all spot 's tissue==1? that my ST data 's tissue position csv 's tissue is all 1,no o,that no backgroud spot
#16
hwbdhuidhcoi
closed
1 year ago
3
Issue due to missing spot barcodes in raw matrix
#15
mattcai10x
closed
9 months ago
10
How to modify strength of SpotClean?
#14
cf98
closed
1 year ago
5
Questions about the output
#13
cf98
closed
1 year ago
1
Questions about tissue regions
#12
cf98
closed
1 year ago
2
bug fix for SpatialExperiment
#11
zijianni
closed
1 year ago
0
SpatialExperiment::spatialData now deprecated
#10
jmvera255
closed
1 year ago
1
Error in optim(x_init, .fn_optim, .gr_optim, method = "L-BFGS-B", obs_exp = obs_exp, : non-finite value supplied by optim
#9
parkjooyoung99
closed
10 months ago
15
Update tissue_csv_file loading for SpaceRanger V2
#8
zijianni
closed
2 years ago
0
Adapt to Spaceranger 2.0 output
#7
jeramand
closed
2 years ago
1
install for R <= 4.1.3
#6
alikhuseynov
closed
2 years ago
3
BayesSpace after SpotClean
#5
JihyunKiminGithub
closed
2 years ago
3
Pixel removal issue
#4
JihyunKiminGithub
closed
2 years ago
2
Fix typo for cauchy kernel
#3
hpliner
closed
2 years ago
0
v0.99.4 supports SpatialExperiment class
#2
zijianni
closed
2 years ago
0
Running SpotClean on all genes
#1
cnk113
closed
3 years ago
5