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batchelor
•
reset
0
votes
6
replies
634
views
fastMNN reproducibility across machines when using Docker
batchelor
9 months ago
nils.eling
• 0
4
votes
2
replies
1.0k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
20 months ago • updated 19 months ago
Guandong Shang
▴ 40
0
votes
4
replies
1.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 19 months ago by
Aaron Lun
★ 28k • written 20 months ago by
Guandong Shang
▴ 40
1
vote
5
replies
1.1k
views
batch effect
TargetScoreData
batchelor
written 20 months ago by
Syed Zaheer
▴ 10
2
votes
7
replies
1.4k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
21 months ago
pcantalupo
• 0
2
votes
2
replies
921
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
2.5 years ago
p.joshi
▴ 40
0
votes
2
replies
1.3k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular
zellkonverter
batchelor
updated 3.2 years ago by
luke.zappia
▴ 50 • written 3.2 years ago by
jma1991
▴ 70
0
votes
2
replies
1.4k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
3.3 years ago
jirkanov
• 0
1
vote
1
reply
949
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.4 years ago by
Adrien
• 0
2
votes
3
replies
1.7k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Angelos Armen
• 0
3
votes
3
replies
2.3k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
ATpoint
★ 4.0k
2
votes
6
replies
1.1k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
Angelos Armen
• 0
2
votes
1
reply
1.0k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
ATpoint
★ 4.0k
3
votes
6
replies
2.8k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
heir_of_isildur88
• 0
2
votes
1
reply
970
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
rmf
▴ 20
3
votes
3
replies
1.3k
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
tahvdbrand
▴ 10
1
vote
2
replies
1.3k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
sorjuelal
• 0
0
votes
4
replies
982
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 13 months ago by
Ivo Kwee
• 0 • written 4.0 years ago by
jashmore
• 0
2
votes
2
replies
1.5k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 20 months ago by
Guandong Shang
▴ 40 • written 4.2 years ago by
heir_of_isildur88
• 0
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Comment: fgsea fork
by
Sofa
• 0
Workshops and summer schools offer immersive learning experiences outside traditional academic settings, catering to diverse interests and …
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
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transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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