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batchelor
•
reset
3
votes
6
replies
2.9k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
heir_of_isildur88
• 0
3
votes
3
replies
2.4k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
ATpoint
★ 4.0k
0
votes
4
replies
2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 20 months ago by
Aaron Lun
★ 28k • written 21 months ago by
Guandong Shang
▴ 40
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Angelos Armen
• 0
2
votes
2
replies
1.5k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 21 months ago by
Guandong Shang
▴ 40 • written 4.3 years ago by
heir_of_isildur88
• 0
2
votes
7
replies
1.4k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
22 months ago
pcantalupo
▴ 10
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
3.4 years ago
jirkanov
• 0
0
votes
2
replies
1.4k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular
zellkonverter
batchelor
updated 3.3 years ago by
luke.zappia
▴ 50 • written 3.3 years ago by
jma1991
▴ 70
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 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
sorjuelal
• 0
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
5
replies
1.2k
views
batch effect
TargetScoreData
batchelor
written 21 months ago by
Syed Zaheer
▴ 10
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
4
votes
2
replies
1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
20 months ago
Guandong Shang
▴ 40
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
ATpoint
★ 4.0k
0
votes
4
replies
1.0k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 14 months ago by
Ivo Kwee
• 0 • written 4.1 years ago by
jashmore
• 0
2
votes
1
reply
1.0k
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 4.7 years ago by
rmf
▴ 20
1
vote
1
reply
997
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
Adrien
• 0
2
votes
2
replies
958
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
2.6 years ago
p.joshi
▴ 40
0
votes
6
replies
693
views
fastMNN reproducibility across machines when using Docker
batchelor
10 months ago
nils.eling
• 0
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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