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fastMNN
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1.1k
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
12 months ago
José
• 0
0
votes
3
replies
1.7k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
3.0 years ago
Madiha
• 0
4
votes
2
replies
1.8k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
3.2 years ago
Guandong Shang
▴ 40
0
votes
4
replies
2.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 3.2 years ago by
Aaron Lun
★ 29k • written 3.2 years ago by
Guandong Shang
▴ 40
2
votes
2
replies
1.6k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
4.1 years ago
p.joshi
▴ 40
3
votes
1
reply
1.7k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 5.3 years ago by
Aaron Lun
★ 29k • written 5.3 years ago by
ATpoint
★ 5.0k
0
votes
0
replies
894
views
fastMNN reconstructed matrix
fastMNN
Interpretation
5.4 years ago
mloza
▴ 10
2
votes
1
reply
1.5k
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 5.5 years ago by
Aaron Lun
★ 29k • written 6.2 years ago by
firestar
▴ 20
1
vote
2
replies
2.0k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 5.6 years ago by
Aaron Lun
★ 29k • written 5.6 years ago by
sorjuelal
• 0
1
vote
2
replies
1.8k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN
fastMNN
mnnCorrect
updated 7.3 years ago by
Aaron Lun
★ 29k • written 7.3 years ago by
tobi
• 0
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
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