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Showing :
batchelor
•
reset
2
votes
2
replies
308
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
8 months ago
p.joshi
▴ 20
0
votes
2
replies
495
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular
zellkonverter
batchelor
updated 16 months ago by
luke.zappia
▴ 50 • written 16 months ago by
jma1991
▴ 60
0
votes
2
replies
534
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
17 months ago
jirkanov
• 0
1
vote
1
reply
417
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 18 months ago by
Aaron Lun
★ 27k • written 18 months ago by
Adrien
• 0
1
vote
3
replies
726
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 21 months ago by
Aaron Lun
★ 27k • written 21 months ago by
Angelos Armen
• 0
3
votes
3
replies
922
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 21 months ago by
Aaron Lun
★ 27k • written 21 months ago by
ATpoint
★ 1.2k
2
votes
6
replies
461
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 23 months ago by
Aaron Lun
★ 27k • written 23 months ago by
Angelos Armen
• 0
2
votes
1
reply
383
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 23 months ago by
Aaron Lun
★ 27k • written 23 months ago by
ATpoint
★ 1.2k
3
votes
6
replies
1.0k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 2.0 years ago by
Aaron Lun
★ 27k • written 2.0 years ago by
heir_of_isildur88
• 0
2
votes
1
reply
407
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 2.1 years ago by
Aaron Lun
★ 27k • written 2.8 years ago by
rmf
▴ 20
3
votes
3
replies
406
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 2.1 years ago by
Aaron Lun
★ 27k • written 2.1 years ago by
tahvdbrand
▴ 10
1
vote
2
replies
422
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 2.2 years ago by
Aaron Lun
★ 27k • written 2.2 years ago by
sorjuelal
• 0
0
votes
1
reply
211
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 2.2 years ago by
Aaron Lun
★ 27k • written 2.2 years ago by
jashmore
• 0
0
votes
1
reply
458
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 2.4 years ago by
Aaron Lun
★ 27k • written 2.4 years ago by
heir_of_isildur88
• 0
14 results • Page
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Comment: Italicise
by
Pau
• 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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