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batchelor
•
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0
votes
6
replies
726
views
fastMNN reproducibility across machines when using Docker
batchelor
10 months ago
nils.eling
• 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
21 months ago
Guandong Shang
▴ 40
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 21 months ago by
Aaron Lun
★ 28k • written 21 months ago by
Guandong Shang
▴ 40
1
vote
5
replies
1.2k
views
batch effect
TargetScoreData
batchelor
written 21 months ago by
Syed Zaheer
▴ 10
2
votes
7
replies
1.5k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
23 months ago • updated 22 months ago
pcantalupo
▴ 10
2
votes
2
replies
979
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
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
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
3.4 years ago
jirkanov
• 0
1
vote
1
reply
1.0k
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
Adrien
• 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
2.5k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
ATpoint
★ 4.1k
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
Angelos Armen
• 0
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
★ 4.1k
3
votes
6
replies
3.0k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
heir_of_isildur88
• 0
2
votes
1
reply
1.0k
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
rmf
▴ 20
3
votes
3
replies
1.3k
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 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 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
sorjuelal
• 0
0
votes
4
replies
1.1k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 14 months ago by
Ivo Kwee
• 0 • written 4.2 years ago by
jashmore
• 0
2
votes
2
replies
1.6k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 21 months ago by
Guandong Shang
▴ 40 • written 4.4 years ago by
heir_of_isildur88
• 0
19 results • Page
1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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