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fastmnn
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
17 months ago
Madiha
• 0
4
votes
2
replies
1.0k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
19 months ago
Guandong Shang
▴ 40
0
votes
4
replies
1.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 19 months ago by
Aaron Lun
★ 28k • written 19 months ago by
Guandong Shang
▴ 40
2
votes
2
replies
909
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
2.5 years ago
p.joshi
▴ 40
2
votes
1
reply
1.0k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
ATpoint
★ 3.9k
0
votes
0
replies
531
views
fastMNN reconstructed matrix
fastMNN
Interpretation
3.8 years ago
mloza
▴ 10
2
votes
1
reply
958
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 3.9 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
rmf
▴ 20
1
vote
2
replies
1.2k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
sorjuelal
• 0
1
vote
2
replies
1.4k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN
fastMNN
mnnCorrect
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
tobi
• 0
9 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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