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fastmnn
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
4 weeks ago • updated 29 days ago
José
• 0
0
votes
3
replies
1.4k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
2.1 years ago
Madiha
• 0
4
votes
2
replies
1.4k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
2.3 years ago
Guandong Shang
▴ 40
0
votes
4
replies
2.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
Guandong Shang
▴ 40
2
votes
2
replies
1.2k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
3.2 years ago • updated 3.1 years ago
p.joshi
▴ 40
3
votes
1
reply
1.4k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
ATpoint
★ 4.5k
0
votes
0
replies
704
views
fastMNN reconstructed matrix
fastMNN
Interpretation
4.5 years ago
mloza
▴ 10
2
votes
1
reply
1.2k
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 4.6 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
firestar
▴ 20
1
vote
2
replies
1.6k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
sorjuelal
• 0
1
vote
2
replies
1.6k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN
fastMNN
mnnCorrect
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
tobi
• 0
10 results • Page
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Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
by
rcreed
• 0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di
by
James W. MacDonald
67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Kent
• 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
by
James W. MacDonald
67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Votes
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
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