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fastMNN
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802
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
14 months ago
Madiha
• 0
4
votes
2
replies
866
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
16 months ago • updated 15 months ago
Guandong Shang
▴ 40
0
votes
4
replies
1.6k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 16 months ago by
Aaron Lun
★ 28k • written 16 months ago by
Guandong Shang
▴ 40
2
votes
2
replies
781
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
2.2 years ago
p.joshi
▴ 40
2
votes
1
reply
929
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
ATpoint
★ 3.6k
0
votes
0
replies
428
views
fastMNN reconstructed matrix
fastMNN
Interpretation
3.5 years ago
mloza
▴ 10
2
votes
1
reply
850
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 3.6 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
rmf
▴ 20
1
vote
2
replies
1.1k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
sorjuelal
• 0
1
vote
2
replies
1.3k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN
fastMNN
mnnCorrect
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
tobi
• 0
9 results • Page
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Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
48k
Reitering James' answer, there is no reason not to use `voomLmFit` if you were planning to follow `voom` by `lmFit`. The reason why `voomLm…
Answer: EdgeR: Exact test and glmQLFTest produce very different results
by
James W. MacDonald
64k
You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.
Answer: limma::voom vs edgeR::voomLmFit - when to use?
by
James W. MacDonald
64k
The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…
Comment: 'Subtracting' counts on basis of Negative control media and water samples
by
Karthik
• 0
I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
by
James W. MacDonald
64k
It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…
Votes
Answer: limma::voom vs edgeR::voomLmFit - when to use?
A: DSS understanding delta option and posterior probability
Comment: Ensembl down???
Answer: How should I run ssGSEA Hallmark Enrichment Analysis?
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
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