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batchelor
•
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0
votes
6
replies
626
views
fastMNN reproducibility across machines when using Docker
batchelor
8 months ago
nils.eling
• 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
1
vote
5
replies
1.1k
views
batch effect
TargetScoreData
batchelor
written 19 months ago by
Syed Zaheer
▴ 10
2
votes
7
replies
1.4k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
21 months ago • updated 20 months ago
pcantalupo
• 0
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
0
votes
2
replies
1.3k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular
zellkonverter
batchelor
updated 3.2 years ago by
luke.zappia
▴ 50 • written 3.2 years ago by
jma1991
▴ 70
0
votes
2
replies
1.4k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
3.3 years ago
jirkanov
• 0
1
vote
1
reply
937
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
Adrien
• 0
2
votes
3
replies
1.7k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Angelos Armen
• 0
3
votes
3
replies
2.3k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
ATpoint
★ 3.9k
2
votes
6
replies
1.1k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Angelos Armen
• 0
2
votes
1
reply
1.0k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
ATpoint
★ 3.9k
3
votes
6
replies
2.8k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
heir_of_isildur88
• 0
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
3
votes
3
replies
1.2k
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
tahvdbrand
▴ 10
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
0
votes
4
replies
971
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 12 months ago by
Ivo Kwee
• 0 • written 4.0 years ago by
jashmore
• 0
2
votes
2
replies
1.4k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 19 months ago by
Guandong Shang
▴ 40 • written 4.2 years ago by
heir_of_isildur88
• 0
19 results • Page
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Comment: BioC2024 abstract submission is open!
by
howell
• 0
What are the conditions for approval of people in difficult circumstances? I want this scholarship
Comment: European Bioconductor Conference 2023 planning
by
william
• 0
[@MariaDoyle][1] Without a doubt. In that position, I will be included in the discussion. [1]: https://support.bioconductor.org/u/239…
Comment: Problem converting msigdb Human symbols to Zebrafish in gmt format
by
Georg
• 0
Thank you for the detailed response. The code worked right away. I appreciate the quick response.
Comment: Error in ImportRData
by
ulna
• 0
[@alastair.fortune][1][gorilla tag][2] The most recent version of IsoformSwitchAnalyzeR available on Github (v. 2.01.13) allowed me to reso…
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
ulna
• 0
[@ilayahari][1][basketball stars][2] The complete version of GEOmetadb cannot be downloaded, even though the demo file works. [1]: http…
Votes
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
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
A: HLA genes missing from TxDb.Hsapiens.UCSC.hg38.knownGene
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