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batchelor
•
reset
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 • updated 21 months ago
pcantalupo
▴ 10
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
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
0
votes
6
replies
669
views
fastMNN reproducibility across machines when using Docker
batchelor
9 months ago
nils.eling
• 0
1
vote
5
replies
1.1k
views
batch effect
TargetScoreData
batchelor
written 20 months ago by
Syed Zaheer
▴ 10
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 20 months ago by
Guandong Shang
▴ 40
0
votes
4
replies
1.0k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 13 months ago by
Ivo Kwee
• 0 • written 4.1 years ago by
jashmore
• 0
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
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
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
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
2
replies
940
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 • updated 2.5 years ago
p.joshi
▴ 40
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 4.3 years ago by
heir_of_isildur88
• 0
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 • updated 3.3 years ago
jirkanov
• 0
0
votes
2
replies
1.4k
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
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
2
votes
1
reply
1.1k
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
2
votes
1
reply
988
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
1
vote
1
reply
982
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
19 results • Page
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Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
Comment: Error using champ.import
by
shilpa
• 0
I'm having same issues too. Did anyone manage to resolve it?
Answer: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
You don't explain how many samples you have (columns of data), but the warning message shown in your post would arise if there are in fact …
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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