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batchelor
•
reset
0
votes
6
replies
837
views
fastMNN reproducibility across machines when using Docker
batchelor
13 months ago
nils.eling
• 0
4
votes
2
replies
1.2k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
24 months ago • updated 23 months ago
Guandong Shang
▴ 40
0
votes
4
replies
2.2k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 23 months ago by
Aaron Lun
★ 28k • written 24 months ago by
Guandong Shang
▴ 40
1
vote
5
replies
1.3k
views
batch effect
TargetScoreData
batchelor
written 24 months ago by
Syed Zaheer
▴ 10
2
votes
7
replies
1.6k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
2.1 years ago
pcantalupo
▴ 10
2
votes
2
replies
1.1k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
2.8 years ago
p.joshi
▴ 40
0
votes
2
replies
1.5k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular
zellkonverter
batchelor
updated 3.5 years ago by
luke.zappia
▴ 50 • written 3.5 years ago by
jma1991
▴ 70
0
votes
2
replies
1.5k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
3.6 years ago
jirkanov
• 0
1
vote
1
reply
1.1k
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Adrien
• 0
2
votes
3
replies
1.9k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
Angelos Armen
• 0
3
votes
3
replies
2.6k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
ATpoint
★ 4.2k
2
votes
6
replies
1.3k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
Angelos Armen
• 0
3
votes
1
reply
1.2k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
ATpoint
★ 4.2k
3
votes
6
replies
3.1k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
heir_of_isildur88
• 0
2
votes
1
reply
1.1k
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
rmf
▴ 20
3
votes
3
replies
1.4k
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
tahvdbrand
▴ 10
1
vote
2
replies
1.4k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
sorjuelal
• 0
0
votes
4
replies
1.2k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 17 months ago by
Ivo Kwee
• 0 • written 4.4 years ago by
jashmore
• 0
2
votes
2
replies
1.7k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 24 months ago by
Guandong Shang
▴ 40 • written 4.5 years ago by
heir_of_isildur88
• 0
19 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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to
Lluís Revilla Sancho
▴ 730
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to
maltethodberg
▴ 180
Scholar
to
Michael Love
42k
Popular Question
to
Leonardo Collado Torres
★ 1.1k
Scholar
to
Gordon Smyth
51k
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