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batchelor
•
reset
0
votes
6
replies
394
views
fastMNN reproducibility across machines when using Docker
batchelor
3 months ago
nils.eling
• 0
4
votes
2
replies
734
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
13 months ago
Guandong Shang
▴ 40
0
votes
4
replies
1.4k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 13 months ago by
Aaron Lun
★ 28k • written 14 months ago by
Guandong Shang
▴ 40
1
vote
5
replies
799
views
batch effect
TargetScoreData
batchelor
written 13 months ago by
Syed Zaheer
▴ 10
2
votes
7
replies
1.1k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
15 months ago
pcantalupo
• 0
2
votes
2
replies
702
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
24 months ago
p.joshi
▴ 40
0
votes
2
replies
1.1k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular
zellkonverter
batchelor
updated 2.7 years ago by
luke.zappia
▴ 50 • written 2.7 years ago by
jma1991
▴ 70
0
votes
2
replies
1.1k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
2.8 years ago
jirkanov
• 0
1
vote
1
reply
796
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 2.9 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
Adrien
• 0
2
votes
3
replies
1.4k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
Angelos Armen
• 0
3
votes
3
replies
2.0k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
ATpoint
★ 3.4k
2
votes
6
replies
904
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
Angelos Armen
• 0
2
votes
1
reply
846
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
ATpoint
★ 3.4k
3
votes
6
replies
2.3k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
heir_of_isildur88
• 0
2
votes
1
reply
781
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 3.5 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
rmf
▴ 20
3
votes
3
replies
1.0k
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
tahvdbrand
▴ 10
1
vote
2
replies
1.0k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
sorjuelal
• 0
0
votes
4
replies
705
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 7 months ago by
Ivo Kwee
• 0 • written 3.5 years ago by
jashmore
• 0
2
votes
2
replies
1.2k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 13 months ago by
Guandong Shang
▴ 40 • written 3.7 years ago by
heir_of_isildur88
• 0
19 results • Page
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Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
by
Mike Smith
★ 6.1k
I'll echo James' suggestion to use the GRCh37 mirror. Most mirrors only have a guaranteed lifetime of 5 years from Ensembl, although it se…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
by
James W. MacDonald
63k
I should also point out that you can find this out by yourself by going to [ensembl][1], clicking on the Biomart link, and then scrolling t…
Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
by
James W. MacDonald
63k
It's my understanding that the archived Biomart data are not complete, which is likely why you cannot get sequences. But you apparently jus…
Comment: ComBat_seq function in sva package does not return a matrix
by
Federico
▴ 10
Thanks for your help, problem solved :)
Answer: ComBat_seq function in sva package does not return a matrix
by
ATpoint
★ 3.4k
That happens if your `x` is a data.frame rather than a matrix. It is listed under the Q&A section in https://github.com/zhangyuqing/ComBat-…
Votes
ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
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